No, to your question, it was exactly what he said, you fit the description of someone they were looking for. Probably someone that just committed some type of violent crime in the area. Either that or your civil rights were violated by the officer. But if he were violating your rights he would have known it at would almost definitely not have stopped at taking your picture for the case file. The picture was most likely for if you decided to sue or claim that your rights had been violated, the officer could produce the picture along with the case regarding the person who you looked like and say, "your honor, it was reasonable for me to pull this man over because he fit the description of the carjacker, rapist, circle-k robber, etc. in these ways..."
I'm a cop and this is what my motivation would have been for taking your picture at the end of a stop like that.