John's not bothered by how close his boys are, in fact, he thinks this is the perfect way to keep them looking out for each other. He knows with the way that they town hop that they can't afford to make any long-lasting connections with people, friends or otherwise. So when Sam is starting to get uppity and is reeling from frustration about not being able to make friends or even consider dating, John is pleased to see that Dean is willing to step in and fill that void for his little brother.
He sees them in the backseat through the rearview mirror, practically glued side by side to each other and he can swear it looks like Sam's hand is in Dean's lap and Dean looks hot in the cheeks, but he says nothing, he just focuses on driving with a little smirk at his lips.
He'd usually give both the boys the beds, but this time he purposefully took one and faced the motel room door with his eyes closed. He hears Dean offer to sleep on the couch but Sam protests quietly, says there's enough room for the both of them and Dean shouldn't have to sleep uncomfortably. He can hear indistinctive soft whispers before it goes quiet, the A/C kicking on and off a few times is the only hum he can hear before he picks up the obvious sounds of lips smacking wet. A mewl. A soft whimper. A soft utterance of 'Sammy' followed by a quiet shush.
He decides to pick up a case the next day, lets the boys know he'll be gone for a couple of days, and leaves them to their own devices, confident that this is all for the best. They need to be each other's everything. It ensured their survival.