If you're looking to save some money and have extra time to spare, you can walk to the bus stop about 3/4 mile from the airport and take the local bus into San Jose, then take the Aquila bus to Todos Santos. Go right out of the airport and cross the road (small cantina/palapa, stop for liquid refreshment), then down the hwy on the left side of the bridge you will see the covered bus stop. It was about 20 minutes and 10 pesos to San Jose. Get off at the 2nd "Centro" stop, look for Calle Valerio Gonzalez, walk across the street from the bus stop, the Aquila bus station is down the street (Calle Valerio Gonzalez) and on the left about 1/2 block down. Ticket to Todos Santos was 80 pesos, I think the bus runs every hour or so, it's the bus going to La Paz but it stops in Todos Santos bus station. Great ocean views on the bus ride.
The road from Cabo San Lucas to Todos Santos and then to La Paz, is a wonderful experience, deserted beaches, the Sierra Laguna mountain range and specially the Cacti makes this trip a very pleasant drive.