Really? Speaking purely on the basis of atheists, the impression I get is that many of them just can't wait to jump down the throat of anyone who's religious, take the piss out of them and then deride them routinely. It's certainly not just the "odd one or two". In my experience of life so far, the atheists I've known have trumpeted far more than the religious people I've known.
It's hardly surprising that the Pope, a deeply religious person, looking at the news and seeing British people queuing up to slag off him and his visit, might feel that religion is being forced off the agenda. The comparison with Nazism is very daft, especially given the appalling attitude that the Vatican took towards the Nazification of the Church system, but I can see why he's said it. To an outside looking in, Britain is a very unreligious nation, and he may well link that to the campaigns of Dawkins and so on.
As for your last point, does anyone honestly believe that atheists in modern Britain aren't on an equal footing to those who are religious? Religion is a taboo in Britain today - if any politician mentioned it in the lead-up to an election I reckon it could seriously damage their prospects of being voted in, and you see that today with a complete lack of any mention of it at the top echelons. Compare that to America, where God seems to feature in virtually every presidential speech, and Britain seems generally atheist.
People might quote the census, but a heck of a lot of people will say that they are Anglican Christian when they don't believe in God, don't go to Church, don't really care.