From my perspective it's because the constitution outlines law making as a power given to the legislative branch. To give regulatory agencies the ability to effectively create law by reinterpretation is clearly bad. But to let the courts give broad deference to the executive branch agencies, when challenged on it, is a clear violation of the separation of powers. Beyond that, it is just wrong, in my opinion, for unelected bureaucrats with vested personal interests in these issues to get deference over the people they serve.
Edit: clarification and wording