Weddingbee boards

Lol okay feel free to disregard this, but last year FI and I needed somewhere cheap to stay and we stayed at the Good Nite Inn (now call CitiGarden Hotel) in South SF.  Let me just say, I have high standards for cleanliness, and I was expecting the worst (we were looking for a REALLY cheap hotel) but it was actually quite nice and clean!  So it definitely fails the "but not too cheap" test, but passes the clean test, the cleanliness and quality of the room was way better than the price would imply.  Also, they have a free shuttle to the airport, I think it was like 5 minutes, which satisfies your other requirement :)

Anyway, since you didn't get any other bites I wanted to throw in my two cents, although it's not exactly what you asked for!

There were a couple other hotels nearby as well, and they also had the free shuttle.  So if you want to up the quality and price a bit, google map the Citigarden and pick one in the same lot and you're guaranteed to be close and have shuttle!