The institutional culture of the Air Force is awful - and the worst of any branch of the US armed services by far.
No it's not.
As somebody that's been working in or for the USAF since 1994 I've NEVER seen anybody take sh**t for holding non-Christian views (and I've seen a lot of people, myself included, holding those views). I guess 20 years of living something is nothing compared to reading/skimming 3 articles on the topic in the last 4 years.
As for the OP, of course this is wrong and hopefully this situation will fix it.