I sometimes wonder if Dawkins says these kind of things mainly to confound his critics. Nevertheless, I think he's right: society has become overly sensitive.
On the other hand, this is not, as the Church's communications director said and as Dawkins himself initially tweeted, a freedom of speech issue. The theater chains are private concerns and have the right to whatever policy they deem appropriate. (They currently do not run ads of a political or religious nature – and so would presumably refuse atheist ones as well.) So the theater chains are free to refuse the ad if they want. But of course anyone who disagrees with their policy also has the right to criticize them.
(Dawkins later retracted his claim that the theaters were violating free speech.)
For more, see here.