It means the values you use to discredit religion.Seriously you're not making sense. I want to know what you mean by athist values. The only thing that defines an atheist imo is the "lack" (if you can call it that) of belief in the supernatural.
IOW if you are offering a critique (never mind whether its about religion or not) you are using values.
If you had no values, you couldn't offer a critique or antithesis or whatever