Absolutely. Criterion describes themselves as "a continuing series of important, classic, and contemporary films", not "a collection of the greatest films ever made." Michael Bay - and perhaps moreso Jerry Bruckheimer - are both important when in comes to the modern blockbuster, a subsection of film that deserves its place in the collection.
I will say, though, that I don't know if Bay deserved two entries. The DVD's are stacked and awesome in every way, so I certainly won't complain. I love them, but I do think that according to what Criterion's mission seems to be, it is kind of weird that he's got both of their blockbuster slots. I also wonder why Wes Anderson immediately gets Criterion treatment when his stuff hits DVD. He's great, and again, I certainly don't complain about these DVD's, I'm just curious why he gets that privilege.