can you give specifics? i'm not aware of any direct route between disney and universal (as opposed to the #50 which will run between the TTC and sea world), so it requires a transfer along the line and for that reason only, i wouldn't recommend it.
the public orlando bus system fills a very specific need which doesn't warrant frequent buses. it could take a substantial period of time to go back and forth.
in fact, i once stayed at a hotel right near universal blvd, so you could literally just walk a mile uphill to get to the parks. across the street is a lynx bus stop, but the only route that stops there to go to universal turns onto idrive first and makes it a 50 minute bus ride.