I don't understand. Could someone please explain...?

Argument for (against) discrimination
I was listening to a BBC reporter today on my local NPR station (NPR link here).  He was interviewing people as they came out of a subway station in NY.  The reporter asked people what they thought about the mosque issue.  One respondent gave a very interesting answer.  What about pedophile priests?  Should Catholic churches be banned from neighborhoods with children?  And what about the history of Protestant slave ownership?  Should Protestant churches be prohibited from locating in predominately black neighborhoods? 
And some of my thoughts.  The right has been whining about Obama's violations of various constitutional amendments.  I saw a bumper sticker that read "OK.  Jokes over.  Let's reinstitute  the constitution."  
If anything close to a violation of the constitution had been enacted, or even drafted, there would be lawsuits up the ying-yang (that's a technical term by the way).
Before Obama's swearing-in, extremists went on a gun buying binge, declaring that the new president would ban gun sales out right and thus violate the Second Amendment.  (The verbiage "…a well armed MILITA is clearly irrelevant.  But it's ALL irrelevant in my opinion.  This should be a non-issue, just like abortion rights.  There are already SO many guns in this nation that they could NEVER be eliminated!)
I've heard them argue that his support of Net-Neutrality violates the First Amendment.  (That one I have a REAL hard time with.  The truth of the matter is quite the opposite).
But their arguments against the Freedom of Religion clause, again in the Second Amendment, seem to be in their opinion to be a "special case."  It's OK to violate that one because…?  Well I don't have the foggiest idea on that.  Could someone be so kind as to explain that rational to me?