Why religious tolerance comes first

I've been sitting on this thought for a while, but now it's time to try it out. Religious tolerance is the most important one.
Let me begin with John Stuart Mill:
"Protection, therefore, against the tyranny of the magistrate is not enough; there needs [to be] protection also against the tyranny of the prevailing opinion and feeling; against the tendency of society to impose, by other means than civil penalties, its own ideas and practices as rules of conduct on those who dissent from them ..." (On Liberty, Chapter I Introductory)
Well, we are at a point in Britain that Mill in Victorian England could not have imagined. In On Liberty, Mill begins his main argument in Chapter II with a discussion of "Of the Liberty of Thought and Discussion", assuming that the argument for freedom of the press has been won and arguing that freedom of opinion is a necessary and healthy right. In Chapter III onwards, he argues concerning Individuality - essentially, free action.
In the UK today, the majority opinion, certainly in the elite, would not argue with Mill on the freedom of action to be secured to all men, to develop their individuality as they wish, within certain liberal constraints (I will not enter the debate on Mill's harm principle here, and remain intentionally vague).
But freedom of thought is not secure in the UK, and freedom to develop as an individual is secured firstly by freedom of thought. Now the magistrate is being used by the "prevailing opinion and feeling" to fight against against all who will argue that any action of man within those constraints could still be morally wrong.
In that context I believe religious freedom is the biggest challenge facing us. Religion is under double attack from the "prevailing opinion and feeling". Firstly, it is being privatised: "that's your opinion, what you believe, fine." Secondly, where it expresses opinions on questions in the public square, it is condemned as backwards (issues in medical ethics) or as verging on the illegal (particularly homosexuality). I remember hearing Sir Iqbal Sacrani very carefully state the Muslim position on homosexuality on Radio 4 and knew that he would be accused by someone of a hate crime simply for doing so. He did not encourage attacks on homosexuals, he did not say that they were lesser human beings because of their sexual orientation or even for their acts, which he did say were wrong. He merely said that the acts were wrong. Yet he was accused of stirring up hatred. Why? Because what is really wanted is the rendering of the opinion illegal. Thought policing.
I will grant that for the Britain of the 20th century, the tests of liberalism were questions of racism, sexism and homophobia, and at the street level they remain huge issues. I face and challenge all three on a regular basis at school. As a Evangelical Christian, combatting these forms of intolerance is about whether all people are in the image of God or not, which they are. But for the liberal elite, tempted to thought policing, the challenge is religious tolerance: they need to put it first. Let people say what they want on ethical, social and family questions, from whatever religious or atheistic viewpoint they want. The only rules ought be no ad hominem arguments and no calling on people to act violently against others for their beliefs or actions.
After all, once the liberal destruction of the family is complete and children live in completely unstable homes and go on to live completely unstable lives, someone will be wanting to find the truth that counters the "prevailing opinion and feeling".