Avoid this place on a busy night.
Flying Tomato has good pizza and the best calzones I have ever had. Unfortunately, their delicious food is marred by the horrible service and high wait times. If there is more than one person in front of you in line, expect to wait over an hour for a pizza. Late on a Friday night, I ordered a calzone, waited for an hour and a half, and was told that my order had gone missing. They made no offer to help me get something to eat, they just ignored me and went about other business. I finally got my money back 30 minutes later.
The staff is discourteous and out of touch with the customers. In my brief words with the manager, I got the impression it was my fault the restaurant was having such a hard time keeping up. In fact, everyone around me was trying to get their money back too after waiting for hours. The service is typically Austin, with disconnected employees who seem to care more about when the next smoke break is than making sure a diner has forks for their salad. The moral of the story is that you should steer clear of this place if there's a chance of it being crowded. If there's no one there and you don't mind impolite sloppy service, it is a good place for some pizza and wine al fresco. Also, consider calling in your order to avoid the lines.