When Qui-Gon asks Shmi about Anakin's Father, she tells him there was never a man involved. Why is Qui-gon so quick to accept such a miraculous story? He didn't even bat an eye, but took her at her word from the start. Why didn't he even question it and try to verify it was true instead of accepting it as a given?
There are a number of reasons.
First of all, he doesn't accept it as truth, only plausible. When he is talking to other Jedi, he mentions only a "possible" birth through midichlorians.
Secondly, he very well could have been using Jedi tricks to learn that she at least thought it was true. If she thought it true, there wouldn't be much he could gain.
Lastly, Jedis are in complete control of their emotions. He must have realized that reacting would not help him, so he didn't.
Maybe he noticed that he had touched a very sensitive point. Shmi was a slave and lived in a very harsh planet visited everyday by pilots, bandits and all sorts of people. What if Ani was the result of a forced intercourse? I say that because I always see some embarrassment both in her answer and in Qui-Gon's expression - as much as you can see expression in a Jedi - right after he asks the question. Anyway, my guess is that Palpatine has something to do with that, maybe he made her believe there was no intercourse just to make the Jedi believe Ani was the one of the prophecy.
Darth Plagueis "influenced life" in Shmi Skywalker and created the most powerful jedi to have ever existed. BOOM. Check out Star Wars Episode 3, the scene to look for is the one where Darth Sidious talks to Anakin while he is trying to entice him to join the dark side. It took me one snow day and all 6 movies in a single day to understand this.