Shia, in the fiction world is called an audience surrogate actor.
Basically, his entire existence in any role is to represent the audience's understanding. He thinks superficially, perhaps sometimes showing times of brilliance in one aspect, always responds to situations honestly (like surprise when something pops out, questioning something that's complicated).
Think also about his looks, he can pull of "surprised" very well, which is what companies want the audience to feel. Furthermore, he has the looks of your average American composite. Average features, average voice, average height, etc.
Basically, shia is you. Therefore, you hate yourself :D
But seriously, if you hate shia like I do, it's likely because he is inconsequential to every film, and his existence is a mockery to the people watching it.
To make it clearer, if you were to see a movie without shia, Shia is "that guy" in the audience who provides a running commentary.
Consequently, if you're making a movie where you think the story is too wacky, you tack on an actor like Shia and everything is supposed to be fine. IMO though, Shia has ruined nearly every movie for me that he's been in. Though it's not his fault for Indy.
An example of a good audience surrogate is the lead actor in district 9.