If you take the cruise transport, don't you still have to find your bags and take them to the bus being used by the cruise? How is this different from if you go by taxi instead?

I'm not a fan of cruise provided transport. You have to wait until the bus is full before they leave.Then when you get to the airport, you have to wait until they unload all the bags from the bus, find yours and go check in.

I have never done the transport in Venice but as long as the taxi company is reliable I can't see why there would be any advantage to taking the cruise transportation.