This is something I've been thinking about lately, but apologies if it's a bit half-baked. Part of what makes the Disney parks special is what they offer that's superfluous to the experience. In the past, that's been things like the Magical Express, free parking for hotel guests (now reinstated in Orlando) and, of course, free FastPass. Losing those things hurts not just because you used to get them for free (although, duh), but because it's been paired with Disney charging a luxury price for what now feels like flying coach.
I think these transportation attractions, along with Rivers of America, fit into this category. Few people are buying a ticket to ride the Main Street Carriages, Red Car Trolley or the Liberty Belle. But the fact that these attractions exist creates a sense that there are things available in excess of the E-Tickets that command such a high price.
That's in addition to the vitality that these attractions give to the parks. It's what makes them feel alive, and losing them will make the parks worse — even if it will be challenging to pinpoint why for most guests.
There's also the Walt angle, of course. The trolleys were added to make California Adventure feel more like a place Walt Disney had a hand in. His skepticism about the ways the automobile impacted American life and genuine affection for public transportation is fundamental to what makes Disneyland, well, Disneyland. I'm not someone who believes we need to view all additions or subtractions through the Walt Disney lens (it's flawed!) but I do think there's a kind of grim irony to removing a relatively recent, Walt-inspired attraction for a Marvel ride.