How do the policies of the War on Terror affect democracy and civil rights in the United States?

Not much at all.

For example - despite all the claims that the Patriot Act has infringed on your rights - haven't you noticed that nobody can quote the section of the Act that says this?

People have a bad habit of believing things without bothering to check facts.

. Source (s) : I am probably the only person on YA who has read the Patriot Act.