Psychologists have shown that diversity promotes tolerance towards different groups if it catches people by surprise.
... they conducted a series of experiments in which participants (British undergraduates) thought of surprising combinations of social categories such as overweight model, rich student, female firefighter or male midwife.
Thinking of people with a surprising, unfamiliar background led to a reduction of prejudice towards multiple stigmatised groups such as the elderly, disabled, asylum seekers, HIV patients, or gay men. It also fostered generalised tolerance and egalitarian beliefs.
... considering people with a surprising background can encourage lateral thinking and lead to more openness and greater cognitive flexibility.
So what combinations with atheist would promote tolerance toward us among the religious?