You already have a fair amount to respond to, so I'll restrict myself to just one question.
In fact I was speaking more in reference to history classes, which retell the stories of the past during times that were dominated by religious beliefs. Events such as the crusades and stories of Spain's conquistadores who brutally killed and enslaved native americans during the colonization of the americas. However I in no way fault the teachers for teaching on these subjects, in fact they are I find them to be extremely interesting. Instead I was simply using it as an example of how religion in public schools is being presented to students in a negative light.
When the Spanish first met the Aztecs, they discovered one of the most brutal religions the world has ever known, at the bloody height of its power. Human sacrifice was carried out on a scale that is almost unimaginable.
The Spanish responded to this by forcibly converting them to Christianity at the point of the sword, killing thousands, destroying entire cultures (albeit brutal ones) and justifying all of this, in part, by invoking the name of Jesus.
Tell me Serdna, how do you propose we tell this story in such a way that it doesn't make religion look bad?
It is not the fault of history teachers that these events cast religion in an unflattering light. I am no expert on US constitutional law, but I don't think that the 1st amendment forbids the teaching of facts that make religion look bad. I think that you are attempting to cast the 1st amendment net too wide here when you seek to invoke it in reference to secular education that you happen to feel is antithetical to your faith.