You're right, eliminating the infrastructure for fares would save some amount of money, but I'd be surprised if it was really that much of a substantial fraction compared with the actual operation of the vehicles.
I think it's significant, there must be tons of full time employees who are checking tickets, selling tickets, doing maintenance on machines, administering subsidized fare programs etc. I don't think it's 25% or anything, but I wouldn't be surprised it it was in the double digits.
Aside from that, though, it's not as if the money not collected in fares is lost. That's money that people get to keep. It's a direct economic benefit to people using transit, and a smaller indirect benefit to everyone else.
