They don't make a lot of sense. Not to the other members of Glee club, not to Mr Schuester, not to Rachel's parents, and definitely not to the rest of William McKinley High School. When they walk down the hall together, even the football players have to take a moment to decide whether they want to deal with all the aftermath of delivering a slushie facial to the quarterback's girlfriend, even if she is a loudmouth freak who wears hand-me-downs from her Polish grandmother.
Not that Sam could really beat anyone up. He may be abulous, but his guns aren't exactly packing intense ballistics, and he'd rather not get suspended before a football game against Eastern. He would prefer to be able to play in that game, considering the stunt kicker's girlfriend called him queer and Rachel already swore war against her "arrogant, homophobic, snobby, ponytail-wearing self". Insert indignant glare and stomp of her foot here.
But even if Sam doesn't beat them up (and he wouldn't, because of reasons stated above and also because two against one is possibly the worst odds ever minus a no-homo gang bang) someone will. It's usually Puck who delivers the first punch, Finn holding Karofsky's hands behind his back while Artie tapes Azimio's together with stage-quality duct tape donated by the appreciative members of the AV club. They trade off after the first suckerpunch, depending on the day and who's willing to take the fall for it - they try to rotate, just so that Puck doesn't get expelled for violence and Beiste doesn't try to kill Finn for... everything. The point is, you don't fuck with Glee Club. They may be losers and Rachel may be a talkative Jew freak, but she's their talkative Jew freak. And, she's also the girlfriend of the quarterback. So show some respect, you overgrown clowns.
That's not to say that they are some fairytale couple. She still talks too much and he's too concerned with his body and what he eats (though he appreciates the fact that she provides him with high-protein egg substitutes in his morning protein shakes and that she's the only person who can make vegan chocolate sauce seem sexy when it smudges on her top lip after she tries to eat too big a bite of soy-based ice cream) and half the time she terrifies him a little bit with the lengths she'll go to get a solo or win a competition, even if she's assured him five million times that it wasn't actually a crack house. ("It was a halfway house, Sam. That's all. And she really should have checked the address on Google before driving there. Show business is serious! She should be prepared for subterfuge!")
She was never supposed to find out about his monthly ritual, though. He had only told Kurt in a moment of "I don't want to be a dick to the first person who was genuinely nice to me without a motive" about his hair dye, and Quinn had been a moment of... well, his charm. He had to impress the girl, and chicks are always swooned by a dude who can be emotional and honest. Right? Whatever. He wasn't going to tell Rachel. He was going to let her live under the impression that his hair was naturally golden and beautiful and perfect, and he was going to let her drown in the jealous understanding that her hair could never be that fabulous on its own. But Rachel Berry could never just let him do anything the way he wanted to. It had to be her way or the highway.
So when she'd accidentally caught him in his bathroom (okay, to be fair, the door had been open) squeezing peroxide and hair dye onto his locks from a bottle, he'd been fucked. To put it lightly. The look on her face had been hard to swallow - it wasn't even that she was surprised (in fact, he thought she looked a little smug) or upset, more like she had known all along. To her credit, she didn't tell anyone else. Instead, she made him a little calendar, with dates circled for his "appointments", and God himself help him if he missed one.
"Look, Sam. I understand your desire to fit a certain social stereotype - particularly that of the well-tanned, California god, and your abdominal muscles certainly reinforce that idea - but I cannot be expected to date someone who lets his roots show. It is one thing to commit to a look, it is another thing entirely to do so lazily. So I made you standing appointments with my personal hairstylist, who operates out of Columbus, so that you'll never have to worry about missing a dye date. Okay?"
It wasn't okay, but what was he going to say? No, Rachel, I want my roots to show like some kind of Aaron Carter reincarnation? No thanks. He didn't need that kind of crazy in his life, and besides - not that he'd admit it, but it was kind of nice of her to go to that much effort. It was batshit crazy, without a doubt, that she made him a calendar, but still. Kind of nice.