What I did was create a new character that is built in the SuppyCenter. This new unit is called a Courier. By adding a new button to the SupplyCenter (Give $1000) - the Courier comes running out. He is basically a crate and I've made it so your own units can't claim him. He can either run to the designated base or jump into a vehicle/aircraft for a lift. Once he is at the base that is requesting money - the Courier can collide with any vehicle/unit and they'll get their money. Also, each faction gets their own Courier.
Interesting part is that the Courier must be protected at all costs. He can be killed or captured by the enemy (enemy gets your money). If your Courier is killed before he makes the cash delivery - the money is lost forever. You'll have to create another Courier (at your own expense).
I've been playing a few games with it and it really adds a new element to Generals.
Hmm, could you make the command center fire a invisible projectile that flies over like a high speed artillery shell to the other base and gives money when it hits? Either those buildings or the supply centers I suppose.