The following quotes from your post stuck out the most for me:
I am not a believer in any way, shape, or form and tried to be supportive in the beginning but now I feel like it's completely changed our marriage because I'm constantly worrying about how he's viewing my words and actions. I know I look at him differently now too.
It's only been 3 WEEKS and it seems that you're already starting to worry that he views you differently. Have you tried talking to him about this?
He has started going to church by himself and it kind of makes me angry because owning your own business is busy enough and now he's takes more time away from our family to go to church. I know that's not the right way to view it but that's how I feel.
How many hours a week is he in church? One? Three? Ten? How would you feel if he spent that same amount of time working out at the gym or going for a run in the neighborhood?
This sudden new found religion has definitely put our marriage on the rocks
Wow. Only 3 weeks and you're marriage is already "on the rocks"? No where do you even mention that you tried TALKING to your spouse about your doubts and fears.
so if we are in two different worlds now does that mean our marriage won't work?
Of course not. But it's up to BOTH people to reach a mutual compromise about this without resentment building up.
You seem to have a lot of fear about this. You were probably pretty content with the way things were, and now you're afraid that he'll start to view you differently, because YOU are starting to view HIM differently. Did it occur to you that his change of heart just MIGHT be beneficial (instead of detrimental) to your marriage?
A lot of 'religion' is about a philosophy of how to live one's life. For example: The Bible says, "Thou shall not lie". MOST people view lying as 'wrong', whether they're 'religious' or not. But the religious people may view lying as wrong because God said so, where as a non-believer may view it as wrong because it tears at the fabric of society. If you and your spouse both view lying as wrong, but for different reasons, do the reasons really matter?
This only happened 3 weeks ago and it's a big adjustment. It'll take some time to work it out IF you want to work it out. As long as your husband doesn't try to force YOU to start attending church or to believe in HIS beliefs, or you don't resent him for changing his beliefs, then you can both start communicating your fears and needs to one another.
Another possibility is that this is a phase your husband may be going through, and although his faith is strong NOW, it may weaken if he comes upon another trying time. My own husband (now deceased) went through something similar. Believed he had a revelation of sorts. Lasted for about 3 months.
Just something to think about.