Does one make an agreement with the government to conduct business? One has to comply with laws but I don't believe that is the same as 'making an agreement with the government'? 

As for religious tolerance one simply needs to look at the case of the Little Sisters of the Poor and their case against ACA in which their healthcare plan was forced to purchase contraception despite their religious beliefs. A case they won by the way. In that case they proved that they were not compelled to follow the same rules. 

I could also point to past lax enforcement of immigration as well, did those that enter the US illegally follow the established rules others used to legally enter?