Let's address the latter point: what's so bad about religion - apart from its falsity? I'm assuming throughout this post that all known religions actually are false. Well, (1) if you buy seriously and non-sceptically into a religious view of the world - I'm assuming here a fairly comprehensive one, not just a couple of key doctrines such as "the Abrahamic God exists" - then it's likely that your whole life will be lived in accordance with a worldview that is, ex hypothesi, fundamentally and pervasively false. In that sense, everything you do and say will be distorted and your life will be structured in accordance with an illusion. I actually think that's an unfortunate fate, and I'd like to rescue people from it to the small extent that I can (while using nothing but liberal means, such as persuasion and example).
(2) Religions tend to preserve moral norms that may or may not have once been functional in the societies in which they originated, but are certainly not functional now. The result is often a cruel disconnect between the way religion tells you how to live and the way of life that would actually be flourishing and pleasurable - and perhaps better for those around you as well as for you. Perhaps this doesn't matter so much, because religious people can still feel happy, even if their happiness is based on the comforting illusion that they are living the most moral or correct way of life in the service of a deity or a supernatural principle. But, worse, the religious are often eager to impose their way of life on others by means of the coercive power of the state. They are always trying to ban something or other, whether it's abortion, alcohol, divorce, contraception, homosexual acts, stem cell research, rival belief systems, or whatever.
We have some choices here: we can insist on liberal tolerance, according to which the state does not impose contentious religious and moral beliefs - taking some proposals off the democratic agenda and limiting the powers of the state. I think we should do exactly that, but it's not a complete answer.
* First, many religious leaders have no commitment to liberal tolerance; sometimes they merely pay it lip service, and at other times they are explictly opposed to it.
* Second, oftentimes religious and moral beliefs that are not well-founded are nonetheless not actually all that controversial within a particular population, for historical reasons, even though they perhaps should be, since they have little evidence in their support. It can be difficult taking these off the political agenda.
* Third, there are many grey areas, since most moral and political claims that are motivated by a religious worldview can be given some kind of secular translation, even if the translation seems implausible and contrived to sceptics. Weak secular arguments can thus obtain great popularity within an electorate if many people in the electorate have a visceral response that is based more on their religious instincts than on the merit of the arguments themselves.
For these reasons, it is often only the most blatantly sectarian claims (e.g. a claim for compulsory, state-enforced belief in transubstantiation) that end up being removed completely from the political agendas of modern liberal societies. If we really do oppose popular religious moralities, or many aspects of them, we can't trust that religious lobbies and the electorate will favour liberal tolerance across the board, while interpreting the idea of a liberal tolerance in a way that significantly narrows the scope of religious organisations to co-opt the coercive power of the state. We can argue for liberal tolerance, separation of church and state, and similar ideas, until we're blue in the face. But we also need at least some people to attack religion's moral pretensions more directly, and, since the morality may claim to be backed by revelation and authority, that can require attacks on the intellectual credibility of the religion itself.
I think it's healthy that modern societies continue to have a constant stream of high-powered people expressing scepticism about religion, and in many cases backing up their scepticism with arguments. I also think it's healthy when those arguments include arguments about the almost-inevitable tensions between religion and the findings of science. This may not destroy religion, but that's not necessarily the aim. It can help create a social ethos in which there's widespread scepticism about religion's intellectual and moral authority. To me, that's a good thing. It can also put pressure on religion(s) to adapt to social and intellectual change, and to mutate into something more benign. To a considerable extent, this has been happening. There are certainly Christian positions with which I don't have too much of a quarrel (although I see no reason why I should actually believe any of them).
As for framing ... There is some contradiction between the process that I described in the two paras immediately above and any masterplan for popularising science that includes reassuring existing religious demographics that science poses no threat to religion - and so should be more appealing to the religious. I'm afraid that I'm unlikely ever to accept that a masterplan such as Matt Nisbet's - which contains this element - should be allowed to override the great social benefit that comes from a stream of intellectually high-powered people in each generation continually putting pressure on the truth claims made by religion. But if I understood correctly what John Wilkins was saying in his post, I agree with him that all viewpoints on this ought to be put. Although I disagree with Nisbet, I won't try to shut him up.
On the other hand, if he ever tells me to shut up he'll get the same sort of terse and hostile response that he received from PZ Myers recently. To be clear, if someone tried to use the coercive power of the state to prevent Nisbet saying "Shut up," to Myers, I'd defend him (i.e., I'd defend Nisbet). In that sense, but only in that rather weak sense, he has the right to say it. I'm all for freedom of speech. But he doesn't have the right to say it without getting a rude reply. Once it's said, Myers has the same right to reply, as he did, "Fuck you very much." Beyond that point, I think that it's actually quite an appropriate response to "Shut up." When you are told to shut up, the conversation has moved to a meta-level where you need not follow it: no one need feel that they have to justify their actions in arguing for their views, as opposed to giving their arguments for the views themselves.