The bus system in Cancun is very convenient and cheap. That's the first thing everyone mentions to tourists. But what do they leave out?
Fares
The fare is 3 pesos, which works out to about 43 cents US. It is much better to pay in pesos because (reputedly) if you pay with US money it is $1, no change.
The bus driver will make change if you have no 1-2 peso coins. Make sure to hand your fare to the driver rather than tossing it in the fare basket; otherwise, no change. The bus driver will hand you a ticket. Usually this has a coupon for some kind of mild discount. In 2 weeks I didn't take advantage of any of them. You are supposed to hold onto the ticket during your ride. An inspector might jump on the bus and ask to see it. I wish I could say this never happened but in my 2 weeks of riding the bus it did happen twice. The good news is they don't mind if you have to uncrinkle it from a little rolled-up ball.
Some people hand their ticket back to the driver as they get off. This is apparently a tip to the driver who gets to re-sell the same ticket to someone else.
Routes
When you are going down into the hotel zone, you can hop aboard any bus with the sign "zona hoteleres" on the front.
When you are coming out of the hotel zone, only Route 1 and Route 2 go to the downtown area. Route 1 goes to Avenida Tulum and goes down it. You will know you've reached downtown when you see "Rolandi's" restaurant on the right and then a flea market on the right. Route 2 crosses Avenida Tulum at the bottom and you should get off at that point. When I took Route 2, sometimes the driver would call attention to this spot and sometimes not.
For short trips up the hotel zone, you can also try other routes, just remember they are going to turn off someplace before getting downtown.
Don't panic when you see signs with arrows indicating "Tulum", "Xel-Ha", "Coba", and so on. These are the names of archaeological sites a long way outside of Cancun, but they are also the names of main streets in Cancun.
Pick-up and Drop-off
Buses come along every minute or less, so you should never have to wait any appreciable time.
Most areas have frequent blue signs signalling bus stops. For areas with no such signs (such as where a lane is blocked off for road construction), you can signal the driver to stop at a spot where there is room to pull in.
Buses will wait a long time for you to reach them if you are approaching a bus stop while one is there. Sometimes you would rather just wait for the next one but they'll guilt you into jogging to it.
If you are not sure where your stop is, you can tell the driver your destination in advance and they will call out when you arrive.
The driver may let you off between stops if traffic is light and they can pull over safely.
The official way of signalling a stop seems to be pressing a button, but the buttons are only above some seats and often don't appear to work. The better way is to walk right up to the front of the bus and look ready to get off; wave your arms frantically if he drives past your stop.
Comfort
Route 1 has uncomfortable hard blue plastic seats. They are made for people with skinny behinds -- clearly not designed to a North American standard. Take Route 2 if you have a choice, or one of the higher-numbered ones if your trip is only a little way within the hotel zone. All the other routes have softer cloth seats.
The buses are very noisy manual shifts. It looks like the driver is wrestling with a big upside-down 5-wood. You will feel each gear shift. To minimize noise and bumpiness, sit towards the back of the bus once you get past the stage of asking frequent questions of the driver.
11 PM seems to be a popular closing time for businesses. Try to avoid taking a bus out of the hotel zone around this time as the bus may get very packed. Because the drivers are incented to carry as many passengers as they can, they will happily let more people cram aboard.
Time for Bus Rides
I did some timings on typical bus rides (including stops) to see how convenient it really is. You wait almost no time to get picked up but the total time is approximately 5 times as much as taking a taxi over the same distance. At the other end of the spectrum, the 5:14 from my hotel to Plaza Kukulcan takes about 35 minutes to walk.
From - To Time Cumulative Time
Club Med - Omni Hotel 8:24 N/A
Omni - Plaza Kukulcan 5:14 5:14
Plaza Kukulcan - Plaza Flamingo 3:46 8:00
Plaza Flamingo - Señor Frog's 3:36 11:36
Señor Frog's - Plaza Caracol 4:34 16:10