My wife and I just got back from our first trip to Cozumel, and we are fairly new as it was only our second full fledged dive trip.
I suggest reading up in the Cozumel forum below in the Mexico forums, and especially read the thread about negotiating the airport. That was a trip, but reading what to do will make it easy.
I researched recommended dive ops, contacted several, and due to the busy season I was referred on from some of my first choices. There seems to be two types: Big operators, and smaller operators. I dove with both types and both have their strong points. My small OP was Blue XT Sea and the larger OP (but by no means the biggest around) was Caribbean Divers. We enjoyed both, but for different reasons.
The small OP was nice because they could tailor the dives to our skills. We also had much more assistance with gear set up and input into dive locations. We found the service to be excellent. We came to be good friends with the divers and employees on the boat. The boat was fast and it could get to any dive sites quickly, but with a more bouncy ride. The hour long surface intervals were always on a beach, so we could get off the boat.
The larger OP was a different, as the boat was slower and we set our own gear up each day. We enjoyed having more folks to meet and visit with, and although there were 12 paid divers, we divided into two groups by experience, and there were separate dive masters. I had heard concerns about safety with larger operations, but I found Caribbean to be very safe. The dive briefing was the most detailed I've seen yet, and there was a mishap when one in our group (a diver who had no dived in some time) had buoyancy issues and had an uncontrolled descent when she couldn't find her inflator/LP hose. The DM had ensured we entered over the reef, so the DM and other divers helped her off the bottom and she finished the dive. I found them to be a very safe operation, the boat ride was slow but smooth, and we met more people but didn't get to know them as well.
Pick an Op based on what type of diving you want. For a beginning diver, I'd recommend a small OP, as you will have assistance and a more personal experience. I suspect most OPs have good folks, and I'll dive again sometime with either of the two we patronized, but I'd probably choose the smaller OP first as I felt more of a personal connection with the divers and employees.
Enjoy the trip, we sure did!