I think most of the complaints here stem not from the fact that the government is banning this substance per se, but that the government finds that it's somehow its business to regulate what you can or cannot eat. That's not the job of government, since that can too easily lead to excess and abuse. Government can regulate these kinds of things, through taxes, quotas, tariffs, you name it. At least that way it can claim that it's protecting the public good by making other options more viable as well as making up for damages caused by the negative externalities provided by trans fats and whatnot. But an outright ban like this seems rather undemocratic to me.
Edit: And I know that there will be an inevitable comparison to drugs being banned as well, here, and I think that's fair. I, for one, do believe that drugs should be regulated and not illegal, for the same reasons as I stated above. If done right, those who would be willing and able to pay the high costs of their effects could do so, and the government could still recoup the expenses caused by their use of the substances.