Why were there no Muslims in Star Trek? Because it's the future.
Why aren't there any Muslims then?
Although I am very interested in Islam, I could not quite grasp the religion and so I am a secular person. But it's just my personal opinion that people who are religious are old fashioned and have no values.
You are entitled to your religious beliefs, but it's not a reason to think they all should disappear in the future. Hundreds of religions flourish, and it isn't fair to single one out. It pays to not judge these people.