I understand your point and it does indeed have merit.
I have never been bitten by a rattlesnake, but I know rattlesnakes bite people. Therefore I would be very cautious around them.
I would imagine our founding fathers, when discussing religious freedom, had peaceful religion in mind. The religion of Islam, which teaches exterminating infidels (non-believers) is, in my mind, not exactly the religion our founding fathers would welcome into our country with open arms.
And that my friend, is the mental gymnastics I engage in......common sense.