In my years listening to TOOL, there have definitely been some lyrics I have had issues with. Before I go on, I will say, TOOL is NOT anti-Christian!!!!! They are openly anti-religion, "think for yourself, question authority", etc. When Maynard uses phrases that contain "devil", "Jesus Christ", etc., he is not, to my understanding, speaking of them directly, but rather using them as a symbol.
If you have heard the A Perfect Circle (Maynard's former side project) song, "Judith", it at first sounds extremely blasphemous. He says "F your God". But, if you read deeper into it, he is actually cursing "the" God that people from his mother's church worship. She was very ill and continued to be extremely faithful, but people judged her and told her she was sinning and all her suffering was her own fault, etc. Maynard found it very upsetting that people would worship a god who believed such things. Obviously we know God is not like that, but...
On the surface, their lyrics can be very controversial and confusing, misleading, etc. to Christians. And that I do not like at all. Maynard discourages blind faith, or anything of the sort. However, he has said in interviews that he is not anti-Christian. He has even said, on stage, that Jesus Christ was a great person for teaching compassion. That's not to say he is a Christian, but he is not bashing people for being Christians.
I am not saying people should or shouldn't listen to TOOL. It is a personal choice and should only be done if it can be done with a faithful heart- maybe it's possible maybe not.