It's also an opportunity for you to challenge the speaker if there was something you disagreed with. Phrased correctly, a question can make both the speaker and the audience re-think something that was stated earlier.
One thing I see missed sometimes is proper form when asking questions. Standing up, stating your name and where you're from, and thanking the speaker for coming and for taking your question add just a few seconds to your question, but they can go a long way to making the speaker feel welcome. From the tech conference videos I've seen, I think this is something we can improve on in the hacker culture. We know what it's like to offer up our work without appreciation to people who don't understand what we do -- but I want to work on being more appreciative of my fellow developers.