W..
Absolutely you should tell your son's dad that you are going to church and that you will raise him catholic and have him baptized.
Even though you are the "primary" caregiver, it sounds from your post like his dad is (at least semi-) involved in his life.
Would you want him to take his son somewhere every time they were together and teach him something and not even tell you about it?
This isn't about your 'marriage'.... it's about HIS SON. So, the fact that you aren't married any longer is irrelevant. You are co-parenting. Yes, he should be invited to EVERY SINGLE event that involvs his son... the son that you are raising together even though you aren't married and your son lives with you most of the time.
For the record, the fact that he isn't religious might make him MORE apt to denounce the Catholic Church and all the sacraments that go with it. You don't have to believe in one specific religion to dislike another religion. You can be non-religious and still have beliefs about all or specific religions.
Also, the basis of religion is not treating each other with respect. That's the basis of HUMANITY. Religion is about following the teaching of that specific religious leader and doctrine. In your case, Catholicism is the teaching of the sacraments, behaviors and sacrifices based on the leadership of the Catholic Church and the Vatican.
What you will have to decide is if you will be the bigger parent. Will you tell your son his Dad is WRONG since he doesn't believe? Or will you coach your son to have tolerance to accept that other people can have differing viewpoints on many different subjects. How will you help your son handle it when the activities with his dad contradict a religious dictate.... ie during lent when your son's dad serves him meat on Friday? How will you help you son grow up with parents who have two different religious ideologies (NEITHER OF WHICH ARE WRONG).
You can't make your ex-husband and the father of your son be respectful of your views. But you can lead by example and be respectful of his. You could start out with, "I understand that you are not Catholic, but Johnny and I have been going to Church. I feel like this will enrich his life". You can also not argue with him. If he starts being disrespectful, simply say that you aren't going listen if he is yelling, but you're willing to listen to his views if he will speak to you like an adult.
Good Luck