From that article:

Saudi opposition sources said the U.S. use of the kingdom's air bases appears to be part of a deal to exclude Riyad from a State Department list of major violators of religious freedom. Such a determination would have resulted in U.S. sanctions on Saudi Arabia.

So, they let us use their border and we don't apply the same standard to behaviour to them that we want to apply to everyone else.

A few years ago, this thought process had the US funding Iraq's chem/bio weapons program.

"Yes, we know you're a restrictive, repressive government, but we'll support you if you'll help us with this other problem."