Totally agree with you, what’s the big deal? Those public seats are disgusting and absolutely rife with bacteria, there are studies on that. Some reasonably fresh socks (or bare feet) absolutely will not matter there. If anything, your feet will get dirty because somebody’s feces and urine are already on that seat. (they really are)

And for the smell: alright, if there are a lot of people and your feet stink, that’s a no. But the smell usually isn’t great in public transport anyways.