Water taxis leave for the mainland (Belize City) and San Pedro about every two hours for about $25US round-trip. Find the current water taxi schedule HERE.
Flights from/to Caye Caulker go to either Ambergris Caye or Belize City Municipal Airport or International Airport.
Taxis are cruising the island all day, so you can just stop them on the street. You also have a good chance to catch one at The Split (the drivers like to take a break there and enjoy the breeze) or at the water taxi docks.
The rate for all destinations on the island is $5.00 Belize ($2.50 US) per person.
It is more difficult to find a taxi in the evenings, so make sure you ask the restaurant or bar to call a taxi for you before you leave.