For our groups we found the advantages to be:
1) Cheaper
2) More convenient (we picked the pick-up times to/from the port)
3) Variety of pick-up locations - for our 7 day cruises we didn't do Disney but flew in the night before, we stayed at an airport near MCO (not Hyatt due to cost) and they picked us up from there
4) Luggage handling if you want it
For our Wish cruise, we will be heading to the port from the resorts and then direct to the airport so we could use Disney's but for that we'll sill use FL Tours for reasons 1 and 2 above. We don't want to get to the port later than 11:00am or 11:30am. That will allow us to check-in and have a short wait to board and then enjoy lunch while we wait for our room to be available. On a 3-day cruise we dont' want to miss time on the new ship to explore.