Yes it was courageous. Having the fearlessness to stand up to Pain all for Naruto's sake even if it meant meeting death is anything but selfish.
Though you could make the argument that she probably wouldn't have did the same thing for anyone else, I don't really think that's the point here. In that particular moment, there was fair development for Hinata. Whether she got her ass kicked or not didn't matter. She stood up to a strong enemy and risked her own life. That's courageous if I haven't seen it.
Those who can't acknowledge this as a courageous moment are clearly fooling themselves or just blatant haters of Hinata, who knows.