"Tolerance" is not a progressive value. I certainly do not tolerate falsehoods (this is just postmodern relativist bullshit) and this is what Picard spoke out against, the Federation actually allowing this people to believe into a FACTUALLY wrong God (The Mintakans did not abandon their faith, they already did that long ago. It was the errors of the Feds which rekindled this very faith. And please stop the "divine plan" nonsense. With this you can rationalize everything.) like Picard. Same in Devil's Due. This doesn't mean that Picard has issues with people who believe in God.He refers to the Mintakan abandonment of their faith as an "achievement", as if it is a GOOD thing to abandon religion.
Now that may be entirely consistent with GR's militant atheism, but for a supposedly "tolerant" and "diverse" Federation officer to be so utterly bigoted against religion is a low low mark indeed.
As Mojochi has pointed out, Picard is anything but a secular fundamentalist à la Dawkins, Hitchens or Harris (the way you use it "militant atheist" is a nonsensical term, these secular fundamentalists are the only folks I know who advocate violence in the name of atheism). In this exchange with the fake Data in 'Where Silence has Lease' he explicitly says that he is agnostic about death which is in itself a semi-religious statement.
But even if Picard actually thought and said that religion is always a bad thing, so what? I personally think that atheism is more enlightened than monotheism and that monotheism is more enlightened than polytheism but I do not proselytize, advocate that more people should become atheists or that religion should cease to exist. You can have a strong opinion about something without any normative implications.
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