We just took this as well too, with a late flight.
The shuttle boarding area is a little bit of a mess. There is no real line, just a bunch of people with their luggage crammed up on the curb next to a SuperShuttle guy with a Nextel/Walkie Talkie. You just walk up to the guy, give him your confirmation number and tell him you're going to DLR. He asks for the total passengers and that's it.
They wait until they can fit all passengers onto a van. They check everyone's confirmation number if you prepaid, which is a good thing. But they have no efficient way to check it. Pretty much the guy on the Nextel, will call in the confirmation number and with the quality of the speaker/mic being bad, there is plenty of repeats. He'll write the van number on the whiteboard and the time. When the van shows up you pretty much cram next to him to get noticed. Then he'll look around and point to people and go, "you, you and you guys here, this is your van."
Our driver was terrible too, very poor customer service with the luggage. In fact he took a smoke break for 15 mins while we were all in the van. When I got off at my hotel, he made me take someone else's luggage out so that I could get to mine. Yeah, not a huge deal, but should I really be touching someone's luggage that's not mine? If I was of evil nature, I could have taken that person's and mine. I think it took us about an hour total from getting our luggage to our hotel right next to the HoJo (it's only a 10-15 min drive). It's not totally bad, but fairly unorganized. It would be great if there weren't too many people and you know you won't be overlooked, but it's hard to trust. We're not going to miss our hotel, but on the way back to SNA, I was worried I would be forgotten at the hotel. So I actually had the hotel call SuperShuttle to pick us up early, just in case they had a mess in picking us up.
However, the ride back was great, the driver was great and we were the only ones in it. Very friendly and helpful with the luggage. On time, so we ended up being early. He was great. Although base on my experience earlier, I would rather be safe than sorry.
They were the cheapest though, only $17 per person for a roundtrip. I probably would do it again cause of the price and I just have to be patient.