I've not played it, but my reading is that it might be possible to play it as a band of protagonists.
However, the system is pretty flexible. I think you could tone down the protagonist and beef up the bruisers a bit and stick with the one-protagonist feature. Leonardo could be your protagonist and make the rest bruisers.
On the other side, the Foot Clan could be mooks, and (assuming you're doing the cartoon) you've got bruisers for Rocksteady and Beebop and Shredder as a protagonist.
Best of luck whatever you decide.