A while back I saw Transformers 2. Obviously my expectations were not massive, but still, big robots and Megan Fox. How bad can it be? Well, pretty bad actually. But more importantly I was distracted from the start, and not just by a scantily clad Megan draped over Harley.
In the beginning of the movie it is established that the Autobots are now working together with the US Gvt to cleanse the planet of the Decepticons. The movie starts out with one such scene where a decepticon is discovered hiding in a Chinese suburb and chased through the city and finally killed.
First of all, this Decepticon was hiding. Not causing mayhem, not (as far as we know) planning to cause mayhem. He was disguised as a construction vehicle and basically trying to stay away from the Autobots that were trying to kill him (mind you, not kill him for doing anything, but just for being a Decepticon). The following chase caused massive destruction to property and most likely several civilian deaths and injuries.
Second, when the robot is brought down and incapacitated, Optimus Prime gives him a few choice words, then summarily executes him with a shot to the head.
I will admit I am not 100% unbiased in this, since when I grew up my favorite robot was Soundwave, who is indeed a Decepticon, but I feel that even looking at this objectively, Optimus Prime is indeed a villain.