There's a few jumping on points:
1 - start at the beginning with Simon Furman's run - Infiltration is the first trade and it sets up a cold war type situation between the Autobots and Decepticons where they first work covertly on planets. The second trade, Stormbringer is more of a traditional story set on Cybertron. Furman's run progresses through Escalation, Devastation, Revelation, Maximum Dinobots and the first three Spotlight collections. Sadly, his run was cut short, and the various plot threads are resolved quite abruptly between Revelation (for the space plots) and Maximum Dinobots (for the Earth ones).
2 - All Hail Megatron. Set a year or so after Furman's run ends, the Decepticons have the upper hand in the war and the Autobots are on the verge of defeat. This isn't the best series, but it sets up a lot of what follows. Collected in 4 numbered trades
3 - The ongoing series. Set after the war ends in All Hail Megatron, various Autobots and Decepticons are stuck on a devastated Earth, and they have to decide how they deal with humanity now. Collected in 7 numbered trades, the first subtitled For All Mankind. While I liked the ongoing opinions vary. Most people agree it improves when James Roberts starts to share writing duties with Mike Costa near the end.
4 - the current setup. There are two ongoing series - More Than Meets The Eye (recently renamed Lost Light) and Robots in Disguise (recently renamed Optimus Prime). MTME/Lost Light is probably the best Transformers comic overall since the original 80s Furman stuff, it's the semi-comical adventures of the crew of a ship which has left Cybertron to go on a quest (largely to stave off boredom now the war's over), while RiD was originally about the political intrigue on Cybertron, it later became about Optimus Prime's attempts to open diplomatic ties with Earth, hence the title change.