Different kind of "everyone benefits from it." There's "individual people benefit when they pay for themselves and everyone does this" and then there's "everyone benefits from each individual receiving it." Public education etc. is the second one: we all as a society benefit when little Timmy gets educated, so we subsidize it in order to maximize that benefit. Transportation of goods is the first kind. I and all of my neighbors benefit from it, but we each benefit individually. When Bob down the street indirectly pays a few dollars to have some item transported to a store by truck, that doesn't benefit me at all. Likewise Bob doesn't benefit from my usage. "Everyone benefits" just because it's ubiquitous.
In economics terms, you want to subsidize things with positive externalities, because they'd otherwise be used less than the most efficient amount. I don't think trucking has positive externalities. It definitely has negative externalities, which would be an argument for taxing it (which of course we already do in various ways) rather than subsidizing it.