Yeah, you still have to go to the desk and get your keys. You stand in the Online Check-in line, which is sometimes faster, but sometimes slower, than the regular check-in line.
It isn't super-fast, like when the Mariott pre-keys you and you check-in in about one minute. But is is (or is designed to be) faster than the long, drawn-out check-in.
If it is your first time at WDW, I'd go with the long, drawn-out version. Wait, I take it back. I'm not taking a side. Whichever side I take, THAT will be the longer line and then you'll blame me and the anger will turn to bitterness and you'll alienate your co-workers, lose your job and end up living on the streets, selling your virtue for a Mickey bar. I don't want to be responsible for all that.
You have to make up your own mind!