It all depends on whether there's a bus you can get right on when you get to the ME counter, or if you have to wait, how many people are ahead of you, whether your resort is the first or the last stop, etc. I've seen estimates in the neighborhood of 60-90 minutes from landing to resort check-in, on average. The last time we visited WDW, the timing was perfect (got right on a bus and were the first stop, no line to check in, etc.), and I think we were checked in and on our way to our rooms less than an hour after our plane had touched the ground.
Although I've seen mid-day (noon-ish) listed as the busiest time to land, catch ME and check in, that's always when we've arrived, and although there are large crowds, Disney moves them pretty quickly and efficiently.