I perceive them differently because Whole Foods isn't trying to shove their beliefs into the public schools. Everyone should have the right to believe silly nonsense, but no one has the right to impose their beliefs on others, and they especially don't have the right to use the instruments of government to do so.
I agree that creationism shouldn't be taught in public schools. The thing is, under the current system, the government effectively coerces people into sending their kids to public schools, through taxes. So if you want your kids taught differently, you have to double pay either by sending them to private school, or home schooling them.