We start from a position of ignorance, and we incrementally gain new pieces of knowledge. Years ago, we learned about the health risks of saturated fats and moved away from them. More recently, we learned about the risks of trans fats and are now moving away from them. The people at the Center for whatever are updating their position based on the latest findings rather than sticking to outdated facts that have been disproven. I wish more policy-makers would do that.
Our knowledge and understanding of the totality of nutrition and health is still pretty small, in part because there are lots of interacting components and because many aspects of nutrition are correlated with ethnicity and lifestyle. Nonetheless, it has been demonstrated that trans fats are bad for your health, independent of other factors. We shouldn't keep consuming them just because science didn't manage to uncover this fact until recently.