Music games are just like any other video game. They let you pretend to be doing something cool without having to spend ten years learning how to do it for real and with all the boring parts removed. I don't know why so many musicians feel the need to point out that people playing Guitar Hero aren't really playing guitar; I don't see any soldiers constantly complaining that playing a FPS isn't like really shooting or Emeril and Rachael Ray telling us that Cooking Mama isn't real cooking or the bald Six Flags guy saying that RollerCoaster Tycoon isn't real theme park management. Maybe it's just that it's new.
Yes, people who think they can actually play guitar because they can play Guitar Hero are annoying, but rarely are they as annoying as this guy:
Most people are just playing it to have fun by pretending to be real rock stars. Video games are escapism. The people who act like they seriously are rock stars are annoying, but there are people like that in every video game fandom. The incidence of them among Guitar Hero players may be a bit higher than the norm because it, like the PlayStation did in the 90s, has expanded the audience of video games to include a lot more idiot frat boys, the same way that Nintendo is expanding the audience to include moms.
Anyway, to answer the question, they may be motivators for getting into it, and the dexterity one develops from doing high-level songs could be adapted to an actual guitar with enough training, but there are few real transferable skills -- probably even less than FPSs, Cooking Mama, and RollerCoaster Tycoon. I also think that they may inhibit musical skill by not allowing any creativity in the main game. Wii Music would actually be a significantly better game for training musicians -- it takes real creativity and musical knowledge to make something like
this or
this.