By the logic of your argument,  Churches should only enjoy the right to freedom of speech and (expressing) their religion if they pay for it?

So does that mean impoverished people and those living solely off community or government charity, and who don't pay taxes, should forfeit their rights to freedom of speech and religion?  Of course not, because all basic or God-given "rights and freedoms" are inalienable and have no financial cost at all.  Also, as long as Churches don't exceed the significant limit of 5% usage they are well within their Johnson Amendment rights to weigh-in on politics.

With the modest salaries of Catholic priests who provide homilies to their parishioners, and the abundantly low to no cost of posting electronic opinions, I would highly doubt that any priest or Church is violating anything in that regard.  Also, America is not secular as you claim but it is open to all people of Good will, and we'd have no idea what that means w/o God writing it on our hearts!