The drive up I-35 isn't too bad, although it should be a lot easier. The problems are perpetual construction and heavy traffic. But with a rental car, you can comfortably make it from downtown San Antonio to downtown Austin in well under two hours.
Call me biased, but if my whirlwind tour of Texas only afforded me a weekend of sightseeing, I'd forego the side trip to Austin. There's plenty to do in San Antonio for just a weekend. Be sure to see the Alamo and the Riverwalk. And don't miss the two best Tex-Mex restaurants in the world: Paloma Blanca and Rosario's (the non-airport location).