Religion only encourages you to do good deeds.
Pfft, hell no. Islam is not the only religion with a concept of "Jihad", and the way the Canaanites were treated was pretty mean. Check this out.
http://www.evilbible.com/Murder.htm
So you can make the whole religion seem good or do it in the name of Jesus or Allah. The bible says you will go to heaven if you have faith in God. So you can be a racist pedophile and still end up going to heaven. But let's say you donated 50 million dollars and you don't believe in God? You get thrown in with Hitler and Stalin. So I'm for this no religion thing.
Exactly why religion is a bad thing. People commit atrocities thinking that they'll be forgiven, and after they are, they're suddenly superior to say, the rationalist that doesn't bother with this shit. Now that the criminal is superior, he can commit another crime, as long as he knows he can repent for it.
You're wrong here. When people in general conversation say "theory" they usually mean "hypothesis". A "theory" in science means a hypothesis which has been tested over and over again and has become accepted fact.
As much as I agree, theories are much more open to change and debate than laws. But your point remains the same. Just because I see someone kill somebody else and I tell a police officer "I think I saw that guy kill that other guy", it would be wrong for the police officer to tell me "No, not until you irrefutable proof."
Religious people defend their views by saying "Well you can't be sure". The problem being, the only reason why gravity, for example, is not a universal law although there is ample evidence to support it is that there is the slight probability that somewhere in the universe there is an exception. However, you cannot base your argument on that exception, that "What if", because you can pretty much disprove any argument with a "what if" statement.
This is why religion is a bad thing. It is commonly said that religion can tell us more about the universe and our meaning and life than science, and with this mentality most religious people feel content with where they are, because according to the bible, the earth isn't supposed to be that great of a place to begin with, and heaven is where it's at.
Science preaches that we know very little of the universe, and that we should expand and try to learn more about it, and use these discoveries to enhance the lives of those around us, so that their brief stay on earth isn't wasted.
This is my evidence.
During the Dark Ages, a heavily religious time, scientific thought was suppressed and rationalistic thinking was punished. The human race actually retrogressed technology-wise, and we had to rebuild. Now take the modern, secular world. In a world without religion, there is nothing to judge others upon, other than the content of their character. Nowadays, we are making discoveries at a break-neck speed, not for God, but for man.
TL;DR
Religion is bad because it impedes human development. Science encourages discovery and strives to enhance the human experience.