Let me just throw out there that, maybe, his footballing ability and relative defensive weakness (which is overstated, see below*) works better for City than for England.
It takes an inordinately stacked team like France to really highlight the middling competency of this England side, who struggled for possession and any semblance of control against a team setup to hit on the counter-attack. Dier was dire, Cahill over the hill, the Ox more like a bull in a China shop. The whole side were in disarray and yet there he is, the fall-guy, John Stones who is singled out for abuse by a media hungry to berate anyone connected with City.
Yet behind all that is the ignored reality that Stones carries an immense amount of his manager's confidence because he's exactly the kind of CB his system needs. England might need a lumbering hulk who can wall off the gaping holes frequently left by Messrs Dier and Cahill, but City need a footballer who is still capable of stepping up in those few (like perhaps 3) occasions that possession is lost and a defensive shift is required.
(*he won 4 aerial duals, more than any other player on the park. Similarly, he made more successful clearances (4) and interceptions (3) than anyone else, while maintaining a 92% pass accuracy, England's best by a measure)