So when the U.S. military made the leaflet showing a dog wrapped in a Taliban flag they certainly intended that dog to represent the Taliban and not Muslims in general. I think a lot of Americans see the controversy in that light. The blame, if any, for the incident is on the Taliban for appropriating the Islamic symbol for itself, not the U.S. military's mistake in printing the leaflet with a different implication than it intended.
But by the same logic, any time someone draws a political cartoon criticizing Israeli policy using a Star of David, or the official seal of Israel (which features a menorah) is not necessarily being antisemitic. The cartoon could be motivated by bigotry or it could be the result of Israel's own decision to use religious symbols as its national symbols.
(Note: I am not claiming that Israel is the moral equivalent to the Taliban. Pointing out one specific parallel does not mean that I am claiming they are the same or similar in any broad fashion.)