1. President Obama introduced the first episode
Mindless partisanship. Shrug.
2. The Catholic Church of 400-500 years ago was portrayed in a negative light
Appropriately. The church did eventually apologize for prosecuting Galileo. I don't think they've done the same for Bruno.
3. Evolution is discussed at length
Well, that's totally appropriate for a show based on science. If it were based on myths and other flights of fancy then we could talk about something else.
4. There was some reference about the negative impact that Europeans had on North and South America when they showed up 400-500 years ago.
That was half a sentence - a throw-away line.
5. There was some reference to the harm that burning fossil fuels is doing to the environment
Again, based on science.
6. Science and the scientific method are glorified
As they should be. The scientific method is based on simple logic - come up with a hypothesis, check whether the real world agrees or not. It's a basic, fundamental search for truth. What could be more glorious?
There's enough ignorance in the world without deliberately fostering more of it.