Do you actually have examples of this, or are you just beating up a straw man?
http://www.patheos.com/blogs/friendlyatheist/2014/10/12/past...
You do also realize that the IRS has agreed to investigate the tax status of churches participating in such protests? http://ffrf.org/images/jointmotiontodismiss.pdf
As opposed to what? An unintentional endorsement? They perfectly know what the law is and they choose to break it. They have been doing it for decades, because they know the IRS won't do anything.
Hundreds of churches have been caught doing it. How many of them have lost their tax-free status?
http://www.irs.gov/Charities-&-Non-Profits/Charitable-Organi...