It didnt make any sense to have Bumblebee instead of Hot Rod, they are basically the same character anyway but the whole Hot Rod > Rodimus Prime angle is to big to overlook
Bumblebee and Hot Rod do have some noteworthy differences:
1. Hot Rod is more of a fighter, whereas Bumblebee is more of a spy/infiltrator. For that reason, it wouldn't make sense to have Hot Rod take Bumblebee's role in the movie.
2. Bumblebee is the proverbial David in a battle against Goliaths. Even in the movie, where Jazz is actually the smallest Autobot, Bumblebee still manages to seem smaller on many levels, both because of Jazz's larger-than-life personality (let's face it, how many guys would go around taunting Megatron?), and because of Bumblebee's more subdued and world-wearied movie personality. Therefore, Bumblebee's drama comes from the simple David vs. Goliath situation. That suits Michael Bay's directing style, because it's best shown through action.
Hot Rod, on the other hand, has only ever been a little guy in any sense when you compare him to guys like Optimus Prime and Ultra Magnus, which is obviously a very different playing field. Hot Rod's drama seems to come from trying to gain self-control while still keeping his zeal, as well as trying to make up for his mistakes. This is a considerably more complicated thing to show in a movie (probably not helped by the movie TF designs), and with all due respect to Michael Bay, I don't think he could do it.
3. Also, let's not forget that Hot Rod has already had his movie back in the 80s, because the animated movie was basically his movie.
4. Las but not least: I'd daresay that, even before the movie, Bumblebee was more popular than Hot Rod, especially amongst the casual movie-going public. If you had asked the average person before the movie to name three Transformers, I think they'd go with Optimus Prime, Megatron and Bumblebee (assuming they could even name three). Also, there's probably a decent-sized group of people who loathe Hot Rod because he was responsible for teh death of Optimus Prime (I know he made up for it, but I doubt they think of that). I doubt Bumblebee has such a group.
Yeah, there are the basic reasons why Bumblebee was more suited for the movie than Hot Rod. I myself would be interested in seeing Hot Rod in a new movie, but I'm not going to get my hopes up on it.