There are so many tour companies/hostels in San Pedro de Atacama it is incredible, and I've heard a lot of bad stories about the Salar de Uyuni tours. Personally, we had our tour office (can't remember the name) tell us that they only used 2005 or newer Toyotas. We drove an hour is the very nice toyota to the border of Bolivia (in the middle of the desert) where they tried to transfer us to a 1990 toyota that WOULDN'T EVEN START. After deciding that we absolutely would not risk getting stranded in the desert with an SUV that didn't work, we eventually convinced the original driver to take us. It could have been worse, but in the end we had a great time.
I would recommend skipping Uyuni (the town), it's only good to get a cheap meal and a bus ticket to your next destination.