From what I've read thats exactly how they do it. You pay half when they pick you up at the airport then the other half when they bring you back to the airport and I believe they pick you up like 3 hours before your flight? All the times are stated in your confirmation
That's correct. On booking you'll receive two email confirmations, one for arrival one for departure. The departure one will state pick up time at the hotel.
This changed a little while back. You have to pay the full amount on arrival now. This is because of complaints by taxi drivers and pressure brought about by their union SINTRA. Their complaint is that since the return journeys had not been paid in advance the transfer companies were essentially operating as unlicensed taxis and "stealing their customers". One thing I've found in Mexico is people are very protective of what they consider "their customers", even if they aren't. Yet at the same time they have no worries about 'stealing' other peoples customers themselves.