I blame Capcom for not explaing it too clearly, but yes, Breakman IS Protoman.
Heres a little background in case you're interested:
Before the events of Megaman 1, Dr. Light and Dr Wily together create their first intelligent robot able to think and act on its own. They name it DLN#00 Protoman, as it was a prototype. Light gives him a whistle so that he could bistow his love for music on the robot. Unlike any other robot, Protoman was powered by a nuclear engine. Shortly after becoming operational, his engine became unstable and Dr. Light informed Protoman he would need to deactivate him in order to repair the problem. Protoman feared he would not be reactived after, refused, and then ran away. Given the seriousness of the problem, Light had assumed Protoman's enegery had given out, and he had for lack of a better term, died. Learning from his mistake, all the robots he and Wily made from then forth used a different energy storage system based on simple electrical energy. Unknown to everyone, Protoman didn't die, and secretly watchs Megaman's fight against Wily. Protoman isn't actually seen until the events of Megaman 3, where he challanges Megaman to little tests under the alias "Breakman" (yes, from break dancing. keep in mind every damn thing in the original Megaman was some musical pun). Dispite the way it seems in the game, Protoman wasn't working for Wily in Megaman 3, and he was set up by Wily in Megaman 5. His power regulation problem was ongoing and still wasn't repaired even by Megaman 8. There is a noncanon novel taking place shortly after MM8 involving Protman's enegery serge probem in which he finally is repaired, but Capcom never offically resolved the issue. Protoman was evil and worked for Wily only in the American Megaman cartoon.
KaiserWAVE, I love Megaman AC too, but you should really check out the PS2 or Xbox versions instead of the GC one. The GC one has reverse controls (A is fire and B is jump rather than the other way around that every Megaman gave used ever) and no remixed music, making it very difficult to recommend over the other versions. The G4 interview is awesome though, so I suppose the GC version does have some maret. I own Megaman AC for both the PS2 and GC and I beat all the games on the GC version first, but its just a whole lot more fun playing them with proper controls and remixed music, espically in the cases of Megaman 4-6.
Its been a long day for me, so I'm going to post the Megaman 4 discription tomorrow.
Till then...
Cheers