If it was, it would be in the news constantly, like Labour's anti-Semitism. I saw the interview and it felt as much of a slight against BoJo and a bit of a moan, than a hardcore case of rampant Islamophobia. For one, if as you say it's top to bottom, why did Sajid Javid get promoted? I'd think they would prohibit Muslims being ministers if that is the case or not even have Muslims as MPs full stop. Just doesn't stack up to outright hatred - the little Englanders in their clubs, sure. Unlike Labour, where it's all got sadly unseemly
The Sajid Javid argument doesn't stack up considering Labour have had Jewish MPs and senior Jewish Party members.
The Labour issue is running (and rightly so because it deserves it) because the Daily Mail have basically got a hard on over it. They run anything vaguely related to it on an almost daily basis whether recent or many years ago (ie. The picture of Corbyn in Paris). And other media are then picking up on it. The Mirror or Guardian aren't doing the same about the Tory Issues that has been a long-standing accusation and far longer than the Labour anti-Semitism Issue.