Just try fucking saying something to the GM if it makes you so uncomfortable - sheesh. If your character has a trait, good or bad, it's expected to affect how they do in the game, and beauty is no different. Usually it's used as a shorthand for the character being able to get what they want out of people more easily.
Perhaps the GM is just giving her that opportunity, with an NPC that she will be able to manipulate. Or perhaps he's hitting on her by proxy because he's a dick. We don't know, because in reaction to being shown fictional male attention she has to hide in the bathroom. Have the fucking fortitude to deal with the issue like an adult.
On the one hand I actually want to sympathise with the one girl who doesn't want to make waves just because she's The Girl, feeling like she has to go along with things that make her uncomfortable because otherwise she's 'letting down the side' and being weak when there can be some actual egregious, negative behaviour going on from the men around her. But on the other this passive inability to express themselves or to try and make sure that everyone is on the same page and enjoying themselves rarely comes from decent roleplayers, but is why you get things like the X-card and all the other hand-holding, overtly coddling bullshit that's trying to force its way into even casual tabletop sessions between friends.
If her instincts are right and the GM is being a creep, that sucks. But she won't find out by hiding in the bathroom, and it does everyone at the table a disservice to let it fester like this. She has no idea whether it's a miscommunication, or whether the other guys at the table would side with her if it turns out she's right, or if the GM would stop if it's pointed out. Instead she's presuming the worst and making it about her being the odd one out, rather than part of a group - and doing it in a way that inevitably ends in maximum drama if not dealt with as an adult, with a calm discussion first.
She's mindreading these guys who are presumably her friends as being a bunch of negative stereotypes, and not giving them a chance to prove her wrong - or right. Roleplaying relies so much on communication, and it's always annoying when the worst communicators make the rules.
We now return to your scheduled SA-bashing.