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It doesn't send the whole database. It only sends the changes. If there are only changes going one way, this should be pretty quick. But if OmniFocus is both sending and receiving changes, then it does need to do a bunch more thinking and goes much slower.

Make sure you've got the latest version of OmniFocus for Mac, as we've made a few changes there that clean up the data on the WebDAV a bit so OmniFocus for iPhone should be able to sync faster.

I notice in another thread that you deleted the database off WebDAV and your phone to start fresh again. That's what I would have recommended. Did it help at all with the speed?