I've rented from Thrifty at MCO several times and my longest wait for the bus was about 20 minutes.
The Thrifty lot is just off airport property, only about a 5-minute drive from the terminal. They seem to run about 2-3 busses at a time, making stops on both sides of the terminal before going to the lot.
Blue Chip membership is a must; it lets you get into the much shorter Blue Chip line, skip filling out the forms (you fill out a master rental agreement when you join Blue Chip and they keep it on file), and most importantly, avoid the hard-sell sales pitch for additional insurance.
Getting from Thrifty to WDW property is simplicity itself; simply get on the Bee Line and head west to I-4, then get off at the appropriate WDW exit. Travel time about 30 minutes.