This is, of course, a matter of personal opinion. My own view is that the least appealing aspect of religion is its tendency to make people intolerant and overly certain of their own beliefs.
Having said that, it is important for me to admit that religion is not the only thing that can make people intolerant and overly certain. Essentially, anything that requires faith in something that is not provable can do this. For example, people who think their own political party is superior can feel this way. So can people who think their own ethnic group is superior to others.
However, religion is uniquely suited to making people intolerant and overly certain. After all, religion is the only area in which people are told that their opinions are sanctioned by almighty God. If you believe that the being that created the universe has told you how to think, it will be very hard for you to tolerate other people who think in some other way.
I prize tolerance and open-mindedness. I feel that religion can work to make people less tolerant and more close-minded. This is what I like least about religion.