My two basic problems with religion are faith and ignorance.
Faith is a fine and necessary thing to have when rooted in experience. We could not function without taking for granted some things. I have faith in my wife. That comes from having years of experiences with her. She and I could not live together if we did not have some basic trust in each other. I have faith in the medicines I buy - that they are what they say they are, that apart from unforseen allergies they will not harm me, that they will make me better. That comes from knowing the FDA is there and from years of experience. I could not stay healthy without some basic trust in medicine. I have faith in the scientific method. That comes from observing the products of science - technology, medicine, etc. Most importantly, it can be tested.
Faith in gods is blind faith. Nobody has had an unabmiguous experience with a god. Many theists say they have, but it always turns out that there is absolutely no way to verify it was a god. People who claim to have agents of gods (like the holy spirit) counsel them cannot objectively distinguish whether they are bona fide supernatural critters or their own overactive imaginations. When we suggest we apply modern hypothesis testing to the efficacy of prayer, they whip out the con man's mantra - thou shalt not test the lord. Why not? What's the lord afraid of?
On top of that they think they have other evidence. Anomalous healings, weird coincidences, "feelings", "just knowing". None of these things are meaningful data. They are a collection of logical falacies, examples of confirmation bias and failures of analysis.
The second part of the religious problem is it proudly answers questions with ignorance. How did the universe begin? God did it. Well, where did god come from? He just was. Answers nothing. How did people come to be? God did it. Well, how did god come to be? He just was. Answers nothing. How does lightning work? God makes it happen. How? One more question out of you, Mr Heretic, and you'll be burnt at the stake. God is the stupid man's answer to relevant questions. It is essentially an invitation to shut up and stop asking questions.
Religion keeps us stupid.