As a Humanist and a skeptic, while I may disagree with tenets of a particular religion, I would never support attempts to outlaw the following of that religion - so yes, I and many atheists support freedom of religion.
While we may criticise and engage in debates to help people change their mind and point out contradictions, having a person jailed, sued or persecuted simply because they hold a particular religious belief is not in line with Humanist principles.
We would only raise an objection when people or organisations use religious freedom as an excuse to harm people (be it emotionally, physically, intellectually, etc) or to impugn their rights. For example, a government employee citing freedom of religion to deny a couple a marriage license simply because the marriage (despite being legal) doesn't line up with that particular employee's religious beliefs, or (more egregiously) when school boards/education departments citing "Teach the controvery!" or "Get your hands off my Bible!" to try to teach Intelligent Design/Creationism as a scientific alternative to the theory of evolution, or (most egregiously) where a church authority believing (in their religious expression) that their faith is more important than the law, decides not to report child abuse - these are examples where freedom of religion becomes a problem.