Simple: because someone influential on the production side of things is quite religious. So, we get a very preachy, manichean Star Trek show that completely contradicts the humanist vision depicted in TOS&TNG.
You just learn to ignore the horrible religion-heavy episodes ("The Reckoning" had unintentional comical value, though)
The Reckoning is a beautiful episode that teaches us that Force Lightening comes in two different colours.
