I thought it strange that a supervillain would call himself after something I knew to be a car engine part.  "Magnet" seems more obvious.  So I have sympathies for Jim Shooter.

But after I learned the official pronunciation, I began using it.

Strangely, while I now pronounce the name as Mag-neat-oh when speaking about the character to others, in my head I still "hear" it as Mag-NET-oh when I think about the character.

=

By the way, when I met Fabian Nicieza at a comics convention, the Marvel Booth was strangely not occupied, so I could walk up to him directly and saw his name tag.  After saying how good it was to meet him, I asked how to pronounce his last name.  He chuckled and asked me how I thought it was pronounced.  Which I got wrong, but he said it was very close and then told me the real pronunciation.  But that then got us and another Marvel staffer into an extended conversation on how to pronounce the last names of almost everyone who every worked at Marvel.  They even tested me on a lot of them.  I think I got everyone's right except for Bill Sienkiewicz.  This was maybe in 1992 or 1993.