After the events of Days of Future Past, in the new future Magneto is not seen and is not mentioned. Here is my 3 reasons where Magneto is.
Reason 1.
He might be exile. Think about it. A man that crazy could be exiled very easy. He could kill another President, or destroy another White House or recruit a new Brotherhead of Mutants and them be ultimately killed and then blame it on Charles because he didn't follow his beliefs.
Reason 2
He might be in Prison. He has been in prison so many times before in the new timeline and in the old one. What's to say he isn't in there again. I mean the Michael Fasbender Magneto may have commited so many crimes that they locked him in another plastic prison. We will wait and see.
Reason 3
He might be dead. This is the most likely option. If he has commited so many crimes and he has escaped a lot of plastic prisons that Charles Xavier may have just killed him. If Charles did kill him, he must of did something so bad that he would kill his former best friend.
These are all reasonable reasons. Any of these could be true, we will just have to wait and see.
Thank you for reading,
Thecomicsmasher.