How The FDA Violates The Seperation of Powers

I was reading an article about the FDA and their decision about whether or not to allow Plan B contraceptives to be sold over the counter and the thought came to me that Congress is the only federal government body to legally have the right to make rules that effect individuals outside their organization. Please look at this cite from the U.S. Constitution to see what I mean.

Article 1 Section 1. All legislative powers herein granted shall be vested in a Congress of the United States, which shall consist of a Senate and House of Representatives.

So as regulations are legislation how did a executive body like the FDA get to start violating the Constitution with impunity. If the FDA has the power to enforce these regulation they place on the food, drug, and alcohol industries then they would fall under the executive branch, but any regulations would still need to be passed by Congress as is the case with the FBI and federal criminal law. The IRS and other organizations that regulate those outside of the federal organization would be treated likewise. The judicial powers in all cases would of course still be retained by the federal courts.