I think your son probably just falls asleep because he was already tired and that's why he was fussing, not because he is exhausted from crying for an extended period of time while you left the room. Don't feel bad, you certainly aren't harming him.
I feel horrible when my baby cries in her car seat but sometimes we don't have a choice. Sometimes she'll cry all the way home from an errand and that's up to 15 minutes - I'd never let her do it in the crib but she isn't hurt in the car seat, she just wants to be held all the time. I try to sing to her and give her toys and make sure her seatbelt is tight enough but not too tight but she still doesn't like the car seat.
It breaks my heart to hear her cry but our first priority has to be keeping all of our kids safe and meeting their needs. Beyond that, yes, sometimes the babies will cry. They don't know that we know best - that sometimes they need to sit in a car seat, or wait for you to take older brother to the potty or rescue older brother when he scrapes his knee. Their crying doesn't mean we are doing something wrong, it's just their only way of communicating right now so if they aren't happy about waiting of course they will cry to let us know.
I think the difference between crying and learning that they don't *always* get needs or wants met instantly versus learning learned helplessness is that if they were learning learned helplessness they would stop bothering to try to communicate to us at all, or be unhappy most of the time.
Even if my baby cries in the car for longer than I'd like a few times a week that doesn't stop her from communicating the rest of the day when she wants down to play, wants milk, needs a diaper, or is tired. She's not learning to just give up and stop trying to express her needs, she's just learning that sometimes she doesn't get what she wants the second she wants it. I don't think that's damaging - if it was, we'd all be messed up, particularly those of us with siblings.