Because lampooning religion was not the point of the film. It was a buddy-road-trip movie through the American southwest, showing how the lives of several characters are changed through their encounters with a wisecracking alien.
The affect of extraterrestrial contact on established human religious institutions is a long-standing trope of science fiction, and Wiig's character satisfies that goal. Plus, while most Christians do not share the beliefs of Young Earth Creationists, the majority of the viewing audience is likely familiar with those beliefs and will recognize the archetype she represents. I don't think the same can be said for Scientology.
Also, just in practical terms, if you're driving through the southern states, you're far more likely to encounter Young Earth Creationists than Scientologists.
I am the sod-off shotgun.
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