Religion as ordinary speech

Didn't Jefferson worry that putting freedom of religion and freedom of speech separately into the Constitution might cause problems? And has it not when an employer rejects paying birth control insurance coverage for employees. saying that would violate his rights? Odd, since whatever his denomination, another can be immediately brought forth whose tenets do not disallow birth control. That there are so many religions with their sects and denominations makes it clear that religion is just another opinion and as such the courts cannot show favoritism for one interpretation over another. One's beliefs should not shield him from laws applying to all with no theological differences or agreements considered. How can the courts constitutionally favor one religious speech over another or over that of non-believers?