No, you don't HAVE to do online check in. It is optional and you can go to the front desk for check in. It doesn't prevent you from booking ADR's or FP+ if you wait. However, I prefer it because it allows me to put my credit card number in without anyone else handling the card. Obviously, if Disney's computer system gets hacked, I'm still vulnerable, but I don't have to worry that someone will steal it at the front desk (either CM or other tourists).
Sometimes, even if I do online check in, I still have to go by the front desk. For example, I stayed at YC during Food and Wine last fall, and they were giving out parking permits. I got mine at the guard shack going in, but my sister was arriving separately so I went to the front desk to get one for her. Or the quick weekend trip to BWI where I got a lobby level room right over the main entrance, so I went to the front desk before even going in the room to see if it was possible to be moved to a quieter location. It was, and they did. Or the stay at AoA where I got the room number email, but when I arrived my MB wouldn't open the door. The front desk took care of that too. I have been able to bypass the front desk many times without incident