My fear and suspicion however is that "Al Quaeda" has become a term that is applied whenever there are "people, who happen to be Muslim, who shoot at 'us'."
That may not seem like something that is worth worrying about, but I think it is. When we apply the term loosely like that we aren't just applying a term carelessly. When we do that, we are attributing all the past crimes that we associate with that name to the people that we are calling "Al Quaeda", whether they had any involvement in those past crimes or not. We are further creating a situation where "Al Quaeda" can appear from nothingness, with no connection to previous "Al Quaeda".
Hypothetical example of why I think this is dangerous: If we (for whatever reason) invade Malaysia, and Malaysian Muslims start shooting at us because we have invaded their country. The moment we apply the "Muslim who shoots at us? that is Al Quaeda" logic, those Malaysian Muslims then, in the eyes of the general public, inherit the crimes of Al Quaeda (say, 9/11). All of a sudden we aren't in Malaysia for "whatever reason", but because those darned Al Quaeda (you know, those "9/11 guys") are there, and they must pay for their crimes.