This thread reminds me of the time I told someone he looked like Steve Buscemi...it did not go over well. Oh, or the other time I mentioned to a guy that he looked like Philip Seymour Hoffman. I did not and do not consider it an insult. Just because they don't look like Tom Cruise (or whatever conventionally attractive celeb) doesn't mean they don't have something attractive about them. They are celebrities who appeared in numerous productions - they have "juice" or charisma or whatever. I would recommend taking it in the spirit in which it was offered, which is almost always positive.
I have not ever met a person who would be flattered or pleased with being compared to Steve Buscemi or Philip Seymour Hoffman on looks. Those two actors are beyond simply 'not conventionally attractive' and your contention that it has to do with their vitality makes no difference.
In fact, while you've said you mean it positively, my experience with celebrity comparisons has been the opposite -- in almost every instance that I've witnessed a person being compared to a non-attractive celebrity, it was obvious from the body language and tone of the person doing the comparing that it was intended as a passive-aggressive statement. In some cases (having been a high school girl at one point in my life) I witnessed the actual and specific statement once the target was out of earshot that it was 'sooo funny' how her face looked. People can be terribly mean sometimes.
Moreover, however it was intended, the OP finds it insulting and upsetting and she is well within her right to feel that way. Others have provided great advice so I will refrain from parroting them, but I wanted to point out, specifically and with all due respect, that the idea of 'take it as it was intended' is a recipe for disaster. It the OP is legitimately upset, it will only lead to resentment and hurt feelings down the line. There is another thread where a poster described snapping off at a mean relative -- I would hate for the OP to venture into the realm of actual rudeness because she suppressed her true feelings about a comment.