Houston is a bigger city than Austin. There is dramatically more traffic flying into Houston than into Austin. There are more businesses in Houston than in Austin. As the vast majority of flying is still done by business travelers, they can charge more to land here.
As far as the hotel rooms and rental cars, yes there is a tax added to pay for Reliant, MMPUS and Toyota Center. But much of the price difference you're seeing is driven by the large amount of business travelers coming to Houston.