My oldest boy was like this and still has problems at 9. First and foremost it is a first born thing. They just want to be home and play with mommy. Second, the fact that he didn't do this last year tells me he just might not click with this new class he is in. I ultimately moved my son to a different school and he was a whole different kid. It could be something as simple as he and the teacher are just not a good match or maybe there is one other student that he doesn't get along with. You never know.
What it comes down to is he is only 3 (almost 4) and it is too young to be expected to endure major conflict, especially with school, he has to go for a long time and you don't want this to be is lifelong impression of it.
I know you are worried about teaching him that if he cries you take him home, and I wouldn't suggest you take him home anyways. I would go talk to the teacher and see what his behavior is when you are not there, also, pop in a couple of times unexpected. You might find that maybe he looks fine but is withdrawn and off in a corner playing by himself or avoiding situations. This is something that the teacher may see as a personality trait and not alert you to it.
Basically, trust your instincts, if he is not having fun or if the crying does not subside, it is just not separation anxiety and find him a new place to go.
Good luck!