I'm aware of overhead/indirects. They're not the only source of university funding, especially at public universities where you have tuition, course fees, a tax base, endowments, and a lot of other things, too. But, I'm not sure what you mean by saying it's half to double of research salary. I do know that overheads are typically at least 50% (and that's a very low bound for most institutions) of grant money received per grant.
Naturally smaller institutions are going to spend a larger piece of their pie on something if its price doesn't scale very much compared to a larger institution.
Well, when people say 50% overhead (the lower bound), they mean that the cost to the grant is `1.5*direct_cost`, not that half the grant goes to indirect costs.
Anyway, research is the primary motivation for purchasing journal subscriptions. It does not make financial sense for a non-research institution to subscribe to many journals. So regardless of which budget the subscriptions are formally taken from, they come from, it should be considered a cost of research. Making the system more efficient frees up money somewhere that reduces the cost of (externally- and internally-funded) research.
Naturally smaller institutions are going to spend a larger piece of their pie on something if its price doesn't scale very much compared to a larger institution.