Atheists sometimes make jokes about theists or scorn them - they may be angry, or indignant. The same happens in reverse. These are normal human behaviours and they are not the same as being intolerant. Being intolerant means denying the right to exist to someone you disagree with - or applying sanctions against him which prevent his full participation in society. Being intolerant means preventing that person from expressing his opinions freely in public - or restricting his movements.
Tolerance is a fundamental requirement of democracy - it is the foundation of a pluralist society.
It allows the free movement of ideas and information. It is the engine of human progress and the hallmark of civilised life. It is clear, then that Atheists should tolerate religions and that they should tolerate us. Racists, anti-Semites, sexists and homophobes all attempt to justify their persecution by claiming that their targets are dangerous, dirty, subhuman, and a threat to 'good' people. As gay people we have seen how oppression depends on lies.