The way that the UK forces operate within our democracy is critical both for their standing in society and the health of our democracy. As part of that process the senior leaders of the military have, within their remit, a responsibility (duty?) to provide, on request from our elected leaders, their advice/opinions concerning their Service. That advice/opinion may be given to the PM, Ministers or the HoC Defence Committee (you can find some very good video footage which records verbatim evidence given to the HoC Defence Committee on the HoC website) either aurally or in written form.
It is vital that those who hold the government to account in the HoC ( and vote when applicable on policy/decisions that affect the Armed Forces) have, as near as possible, the accurate information to hand - warts and all. As far as I can see, from the public reports to which we all have access, CinC Air has done nothing more than meet his responsibilities in this area.
I hope that the PM had no intention of suggesting that senior serving officers in the Armed Forces should not be playing their part in ensuring a healthy democracy and therefore that his off the cuff remark was just that. In the circumstances I would hope (as others have mentioned) that the PM should write to Sir Simon to clarify.
Having been privileged to serve on operations under his command it is my view that Sir Simon Bryant is a first class professional officer who serves his country to the best of his, undoubtedly, outstanding ability. One would hope that others who operate within our democratic process could demonstrate the same