Karina is an atheist, but her friends jokingly call her “the prophet.” That is because she is helping nurture a community for unbelievers in predominantly Muslim Indonesia, where trumpeting one’s disbelief in God can lead to abuse, ostracism and even prison. “It’s very normal for atheists to be paranoid because the environment does not support them,” said Ms. Karina, 26, who uses only one name. But, she said, “in this group people don’t need to be afraid.” Indonesian Atheists was founded with a Facebook page in 2008 and now holds regular gatherings. The Internet has offered its members a safe space to air their opinions, and the feeling of community has made them braver about gathering in public. But recent prosecutions of people who made online comments deemed blasphemous by the country’s courts have stoked fears that they too could come under attack. “Members’ growing outspokenness and courage does not indicate that other people increasingly accept us,” said...