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Dean has a whole sack full of reasons why he loves Rory and wishes Jess would fall off the edge of the planet, but right at the top is that he's two entirely different people around them. He likes who he is around Rory. He's responsible and friendly and patient, like she deserves. Around Rory, Dean is honestly a good person. He doesn't have to second-guess his every action, doesn't have to worry if he's doing things for the wrong reason or just doing the wrong things, period, because Rory is his shining upright moral compass, and she always points him in the right direction. With Rory there is only one reason, and it's always right, because it can never be wrong to make Rory happy.
With Jess, there are a million different reasons, because Dean wants so many things from Jess, and most of them are totally wrong. Dean wants to punch Jess in the face for ruining everything by wanting Rory, which scares him, because he's never been a violent person and he's never felt that itchy desire to just hurt someone really badly, hurt them until they go away and cease to be a threat. But Dean can't look at Jess anymore without also wanting to shove him into some dark corner and kiss him until neither of them can breathe. Dean wants to do filthy things to Jess, filthy wrong bad things that he never ever wanted from Rory, and he wants Jess to do all those filthy wrong bad things right back to him. He can be patient with Rory; he's happy to wait until she's completely ready, and when she is he'll have roses and candlelight and he'll make love to her tenderly, like something out of a movie or a song. Dean wants to fuck Jess, wants to push him down, rip off his clothes, and just rut like an animal in heat. He wants to put claw marks down Jess' back, bite marks on his neck, bruises on his wrists - and he wants Jess' fingernails digging into his shoulders, Jess' teeth in his throat, Jess' hands slamming his into the wall. With Jess he wants ownership, complete and total and returned in full.
That's bad enough, to want all those things from Jess that he doesn't, can't want from Rory. But Dean isn't a complete bastard, not even around Jess, and he isn't blind, either. He knows Jess got dealt a pretty shitty hand before coming to Stars Hollow, and he kind of... he feels bad for him. It's not pity; Jess would murder him before he'd be pitied. It's like he used to feel when he saw abandoned puppies in Chicago. He wants to take Jess in and feed him and pet him until the raw edges fade and he doesn't try to sink his teeth into any stranger who comes too close. But Jess isn't like a stray dog; there's no Humane Society for rehabilitated teenagers. There is no one who can give him shots against the violence that shines in his eyes, and if Jess tries to hurt him it'll be a lot worse than a bite on the hand. Even now, Jess knows enough to destroy Dean with a few careless words, and if Dean opens up to take Jess in... Jess could obliterate him.
The weird, sick tangle of emotions Jess brings out in him makes Dean edgy, makes him snap even with Rory. He hates that, hates that Rory has to see the person Jess makes him when he tries so hard to be someone else for her. It makes him wonder, too, because he remembers the last time he was short-tempered and violent around Rory, and sweet Jesus, he hopes he wasn't angry with Tristan for the same reasons he's always angry with Jess, because Tristan was one fucked up pretty rich boy, okay, but he was also a dick, and Dean wants to believe he has standards, even for rivals-slash-fuck-buddies. But he doesn't know, and maybe he never will, and that's Jess' fault, too.
So when he slides out of the car after a week away from Stars Hollow, during which he tried a lot to think about Rory and not about Jess, and pretty much failed, he's relieved to see Rory, because how he feels about Rory hasn't changed. He loves her, and she makes him a good person, and he wants so much to be what she needs. And Jess crashed her car, Jesus, the car he made her, the solid symbol of his devotion but that's a metaphor for another day, is she okay, is Jess okay, and why does Jess always fuck him and Rory up, but Dean's used to the sucker-punch of want to kill him want to fuck him want to make him mine that Jess packs, even in absentia. So he shoves the whole mess of feelings he doesn't want and doesn't know how to deal with away, and focuses on Rory, and being Rory's Dean. Jess is gone, and despite the sick twisting in his stomach that is the remnants of Jess' Dean, things are finally going to be normal again.