Yes if we take the logic to ridiculous ends we can have the state confiscate everything it needs from select individuals, but the problem with that is that it's ridiculous. it's absurd. we can use different logic in different places.

using eminent domain to get land for a shop attached to a train station isn't a slippery slope to the cops coming in and confiscating your car just because they want it.

Taxes and fares aren't enough to run a transportation system properly because of politics and culture.