They do not seem to have been. They did get forced out of their business, but it was in a family quarrel over homeschooling and not by the government. As a matter of fact, they did not even get convicted of the misdemeanor truancy charges (the school district dropped charges), but filed the lawsuit alleging that the charges should never have been filed and that they had an absolute constitutional right to educate their children or not in the privacy of their own home, without providing any documentation whatsoever to any government official. Where it hit the national media in a "the sky is falling" manner is when the court ruled that they do not, in fact, have such a right.
The bar for removal for neglect is pretty high -- especially for immediate removal. Yes, you hear about the occasional case making the news where someone makes a mistake. That is very uncommon. As long as the child is being fed, housed, and not beaten or molested, it's pretty hard to get an emergency removal. If it were routine to remove children for any neglect allegation, I would never call CPS for anything short of molestation that I considered 95% likely or direct physical harm. But I don't think the off-chance is sufficiently high to not call for what *I* would consider a sufficiently serious allegation.