Wow, has this thread taken off in my absence...
I think Chris Patten is wrong, for the following reasons:
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There are no such people as 'atheists'. We do not congregate together and share our beliefs. We would be religious if we did. We are as diverse as people who believe in deities.
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Whilst there are certainly some people on the extreme end of the atheist spectrum who are intolerant (talking about sky fairies and so on), I do not find this to be true of the majority of non-believers.
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The perception of intolerance seems to come (and this is my perception only) from people who are finding that certain structures and systems which have always been based on privileging those who believe one thing over those who believe another, are now being challenged.
Equality legislation is a good example - Catholic adoption agencies, or Bed and Breakfasts, or couples wishing to foster - many are now finding their beliefs held up to scrutiny by a system which says 'actually, we should be defined by our common humanity, not by our religious beliefs'. This is obviously very difficult for some people, but as I said in my much earlier post, we cannot have a just society until we treat everyone's beliefs as equal and worthy, including the lack of belief.
This will mean a lot of changes, and I expect that people on both sides will get it wrong a lot of the time, but it is worth striving for a system that transcends this tribal 'them and us' rhetoric that has so far been the basis of most societies. Right now, Christians feel marginalised because their traditional position of privilege is being eroded by the rise of (IMO) necessary secularism.
Having said all that, we do need some common sense. I don't object to a nurse or a BA worker wearing a visible cross (or kara, or other symbol of their faith). It would be very petty to be offended by such things, and I'm not. I would also not be offended if someone offered to pray for me - I would explain that I am an atheist but that the person in question was of course free to do as their conscience dictated. But not in my presence.
I do very strongly object to people refusing to do their jobs on religious grounds. Pharmacists refusing to prescribe the pill, registrars refusing to officiate at civil partnerships, relationship counsellors refusing gay couples - they have to accept that this is what their job role entails, and that they cannot pick and choose which bits of their job they wish to do.
Even there I would make an exception for people not wanting to take part in ending what they perceived as a life - doctors not referring someone for a termination, for instance. However, I would want such a doctor to be obliged to refer to a colleague who would help, and in a timely manner. The same would apply to euthanasia (disclaimer - I am pro-choice and pro-euthanasia).
I don't see very much intolerance by atheists at all, and in fact my personal relationships with family and friends who believe are harmonious because we all respect each other - it's just that translating this mutual respect into societal structures that work is going to take a long time. We've only just started.