Same happened to us for our trip in on Saturday. Tried both a visa and debit card with the online payment system. My banks CC fraud prevention line said no failed charges were making it through or being rejected on their end. I did fill out the traveler info online and got the email w/ confirmation number to keep from having to fill out in person.
When we got off the plane, everyone on our flight from Houston was funneled through 2 - 4 lines going through an outside checkpoint. After standing in one of the lines for a couple minutes, I asked if this was the line to pay tourist tax and was redirected to a small building on the left most section of the entry point. Inside there were 4 stations taking payments. Everyone going into that building had complained that no online payments had been accepted. The lady that took my payment mentioned that something was apparently broken with the online payment system. I used the same Visa card in person with no issues. After leaving out the back side of the payment building, I got into another line to go through customs / passport check.
My party of 3 were at the back of the full 737 from IAH, so nearly the entire plane deboarded before us. However, the payment and customs process went smoothly and quicker than customs / entry to Cozumel.
Now for the Avis rental… My wife waited for our checked luggage while I made straint line for Avis. There were two customers at the counter and one other in line in front of me at Avis. For no apparent reason, It took longer to get the rental than to pay the tourist tax and go through customs. Lots of Avis employees wandering around behind the counter but no more than one or two employees at times actually attending to customers.