As Ironwave notes, if you want to read "modern" IDW, start with Death of Optimus Prime and then get into More Than Meets The Eye and Robots in Disguise. That's the simplest option.
How do you want to read? Chronologically or in publication order?
The huge IDW hardcover collections begin in chronological order, which leads to some weird insertions (IE reading something featuring a character that wasn't actually introduced until later). Honestly, reading in "chronological" order is probably not the best thing for IDW.
Here is the publication order, as informed by the Transformers Wiki.
To be quite frank, a lot of the material isn't really worth reading. I really enjoy the beginning of Furman's "ations" series but they end up going nowhere. All Hail Megatron is ... divisive, and honestly quite pointless. It's clearly a six issue mini padded into 12. The ongoing by Costa is outright awful. Megatron Origin stinks; it's more interesting to see what Barber and Roberts do with the ideas MUCH later. It becomes better in retrospect. The spotlights are entirely hit or miss. Heart of Darkness is garbage. Autocracy, Primacy, etc, they're nothing special and aren't necessary at all. Windblade was fine. I'm really enjoying Til All Are One.
Last Stand of the Wreckers is probably the "beginning" of modern IDW. It clearly informs what Barber and Roberts would do later and there are reprecussions still to this DAY. Literally, this week's issue of MTMTE. The "Chaos Theory" two-parter by Roberts in the ongoing is also worth reading.
http://tfwiki.net/wiki/IDW_Publishing
The Transformers: Infiltration (2005–2006) Establishes the presence of the Transformers on modern-day Earth and re-establishes the theme of "robots in disguise" as central to the new continuity; a seven-issue story arc (issues #0 to #6).
The Transformers: Spotlight (2006–present) Series of one-shot stories focusing on a single Transformer per issue; this series has no fixed publication format and is ongoing. It went on hiatus after "Spotlight: Metroplex" while the new ongoing series was getting established, but has since returned, although at a greatly reduced pace.
The Transformers: Stormbringer (2006) A four-issue miniseries tie-in to Infiltration, establishing Cybertron's current situation in the re-boot and focusing squarely on the Transformers.
The Transformers: Escalation (2006–2007) Sequel to Infiltration; a six-issue story arc detailing a conflict with the Decepticons in Brasnya and the abduction of Sunstreaker and Hunter O'Nion.
New Avengers/Transformers (2007) A collaboration between Marvel Comics and IDW featuring the first ever crossover between the Transformers and New Avengers. Though it has minimal effects on the overall universe, it was specifically designed to fit into continuity between Infiltration and Escalation.
The Transformers: Megatron Origin (2007) A four-issue story arc detailing the events surrounding Megatron's rise to power and the founding of the Decepticon faction.
The Transformers: Devastation (2007–2008) Sequel to Escalation; a six-issue story arc following up on what happened to Sunstreaker, as well as the Decepticons' battle with the Reapers and seeds are planted for the upcoming Dead Universe arc.
Revelation (2008) Sequel to Devastation; composed of 4 Spotlights; Cyclonus, Hardhead, Doubledealer and Sideswipe. This series wraps up the first set of Dead Universe-related events.
The Transformers: All Hail Megatron (2008–2009) A twelve-issue maxi-series, extended to sixteen to include the All Hail Megatron Coda series. It chronicles the aftermath of the defeat of the Autobots and the Decepticon conquest of Earth. The publication schedule overlaps with Revelation and Maximum Dinobots. Issues 13–16 each consist of two 11-page stories that help strengthen the flaws in All Hail Megatron and tie into the ongoing series.
The Transformers: Maximum Dinobots (2008–2009) A five-issue which takes place chronologically between Revelation and All Hail Megatron (which it was published concurrently with). The series wraps up Furman's story arcs with the Dynobots, Sunstreaker, the Headmasters, Shockwave, Skywatch and the Machination.
The Transformers Continuum (2009) — A one-shot intended as a 'catch-up' for new readers, ahead of the new ongoing series.
The Transformers (2009–2011) An ongoing series which began in November 2009 [1]. The series is penned by Mike Costa with art on the first arc by Don Figueroa. Different artists have contributed as well.
The Transformers: Bumblebee (2009–2010) A four-issue miniseries chronicling Bumblebee's journey on Earth after the events of All Hail Megatron, focusing on the conflicts and decisions 'Bee makes (sort of like a Spotlight). It began in December 2009, written by Zander Cannon with art by Chee Yang Ong (the team that worked on the second story of All Hail Megatron #16).
The Transformers: Last Stand of the Wreckers (2010) A five-issue miniseries which began in January 2010, written by Nick Roche and James Roberts and drawn by Roche with colors by Josh Burcham. It chronicles the actions of the Wreckers in deep space after All Hail Megatron.
The Transformers: Ironhide (2010) A four-issue miniseries covering Ironhide, with story by Mike Costa and art by Casey Coller. It was published from May through August, 2010.
The Transformers: Drift (2010) A four-issue miniseries that chronicles Drift's origins as the Decepticon Deadlock to becoming an Autobot. It's written by Shane McCarthy, with art by Alex Milne and colors by Josh Perez. It was released bi-weekly in September, 2010.
The Transformers: Infestation (2011) A two-issue story set within the larger Infestation, a cross-over in which zombies invade multiple IDW properties. In addition to Transformers, Star Trek, G.I. Joe and Ghostbusters are all invaded by the cross-dimensional zombies. The Transformers segment involves the Autobots teaming up with Galvatron's crew to stop the menace. It is written by Dan Abnett and Andy Lanning, with art by Nick Roche and colors by Joana Lafuente and Josh Perez. The entire series was released weekly over 10 weeks, starting in February, 2011.
The Transformers: Heart of Darkness (2011) A four-issue miniseries featuring Galvatron and crew, following the events in Infestation. It's written by Abnett and Lanning, with art by Ulises Farinas. Released March through June, 2011.
The Transformers: The Death of Optimus Prime (2011) IDW #125 written by James Roberts and John Barber, with art by Nick Roche. Optimus Prime makes a decision about his role in a post-Great War Cybertron.
The Transformers: More than Meets the Eye (2012–present) An new ongoing written by James Roberts, with art by Alex Milne. Following the revitalization of Cybertron and the departure of Optimus Prime, Rodimus sets out to find the legendary Knights of Cybertron with a crew of like-minded Autobots aboard the Lost Light.
The Transformers: Autocracy (2012) A twelve-issue digital comic starring Orion Pax and featuring his transformation into Optimus Prime. It's written by Flint Dille and Chris Metzen, with art by Livio Ramondelli, and was released bi-weekly from January to June, 2012.
The Transformers: Robots in Disguise (2012–present) Another new ongoing written by John Barber, with art by Andrew Griffith. Bumblebee, Starscream, and Metalhawk attempt to forge a government and maintain control on the revitalized Cybertron, while personal mistrusts, old grudges, and new problems seek to shatter the fragile peace. This title was renamed to The Transformers starting with issue #35 to avoid confusion with the new Robots In Disguise franchise, including an IDW tie-in comic.
The Transformers: Monstrosity (2013) The sequel to Autocracy by the same creative team.
Dark Cybertron (2013–2014) — [12 issues] A maxi-series largely within the ongoing series focusing on Shockwave's machinations to change the universe and the powerful repercussions; written by John Barber and James Roberts with a variety of artists.
The Transformers: Windblade (2014) A four-issue miniseries focusing on Windblade in the wake of the "Dark Cybertron" crossover event, written by Mairghread Scott and drawn by Sarah Stone.
The Transformers: Punishment (2014) A five-issue motion comic miniseries starring Optimus Prime investigating a series of murders on Cybertron after the events of "Dark Cybertron", written by John Barber and illustrated by Livio Ramondelli.
The Transformers: Primacy (2014) The sequel to Monstrosity by the same creative team.
The Transformers: Drift - Empire of Stone (2014–2015) — [4 issues] As Drift rights wrongs in the galaxy, he is joined by Ratchet and winds up facing an old enemy. Written by Shane McCarthy with artwork by the Regeneration One team of penciller Guido Guidi, inker Stephen Baskerville, and colorist John-Paul Bove.
The Transformers: Windblade vol. 2 (2015) — [7 issues] Windblade returns in a story advancing the Combiner Wars, trading issues with the main series; at the conclusion of the event, the Cityspeaker helps Starscream seek out the lost colony worlds while trying to prevent the ruler of Cybertron from forming an empire; written by Mairghread Scott and drawn by Corin Howell.
The Transformers: Combiner Hunters (2015) — [One-shot] On the trail of the stolen Enigma of Combination, Windblade and Chromia run afoul of the Torchbearers; written by Mairghread Scott and drawn by Sara Pitre-Durocher
The Transformers: Redemption (2015) — [One-shot] The Dinobots head out into the post-apocalyptic Cybertronian wilderness on a secret mission. Written by John Barber and drawn by Livio Ramondelli.
The Transformers: Sins of the Wreckers (2015–2016) — [5 issues] When Prowl is kidnapped, it falls to the Wreckers to rescue him... but does anybody want to rescue the disgraced Autobot schemer? Written and drawn by Nick Roche.
The Transformers Holiday Special (2015) — [One-shot] An anthology of holiday-themed tales set on Earth, Cybertron, and deep space.
The Transformers: Till All Are One (2016-present) — [Ongoing] Windblade tries to maintain the peace on Cybertron while dealing with the colony worlds and the Council of Worlds. Written by Mairghread Scott and drawn by Sara Pitre-Durocher.
