The department of justice now claims atheism is a religion so now all groups who are anti-religious can now be?

Actually, SCOTUS said a long time ago that when it came to first amendment protections atheism served the same purpose as a religion. The DOJ has nothing to do with any of the stuff you just mentioned, either, so I call "shenanigans". THAT'S what I think about THAT.

Interesting (maybe) aside: there are atheistic religions aplenty, including Buddhism, Confucianism, a most forms of Satanism, Jainism, etc. They are all tax exempt if they form a church and file the paperwork, making them a legally recognized religion/church. You only need two people to form a church, and there are seminars that teach you how to do the paperwork. The Church of Satan is atheistic and has been tax exempt for decades. However, they pay their taxes as an added "fark you, you morally reprehensible slime balls" to the Christian churches around them.

My group is tax exempt, but we pay our taxes anyway as a "gee, it would be a shame if someone set our hof on fire and there were no well maintained roads to drive on or a fire department funded well enough to put it out" kind of statement, as we don't need to poke others in the eye to feel morally superior. The whole behaving ourselves despite the lack of a threat of eternal torment does that for us just fine.

The department of justice now claims atheism is a religion

No..it doesn't...

Any charitable or educational or similar organization can have tax exempt status--even the one organized to teach you about UFOs. You are saying nothing.

There is no separate tax exemption for churches.

Not worth the sacrifice of principle. The vast majority of atheist and humanist organizations and their members do not consider atheism a religion.

Not all atheists are anti-religion. You only have to conform to one thing to be an atheist and that is to reject the claim that a god exists.