The Prime Minister meets the monarch every week. It's very, very naive to assume they only talk about the weather.
The Queen was known to object to legislation that affected her personally. And the monarchy - as the head of the aristocracy, the biggest land-owner, a major influence on the Tory Party, and a private corporation with significant business interests - can always use back-channels and cut-outs to have its say.
The British specialise in this kind of indirect hinting and insinuation. It's part of the culture at most levels, and it drives foreigners insane, because until you learn the subtext you'll completely misread what's being said.