Not really. Most of the worst mutant supervillains weren't motivated by anti-murtant prejudice...
Selene was treated like a sorcerer-queen for millennia... she didn't even knew she was a mutant to begin with, she thought she was a natural magician or demigoddess.
Apocalypse was enslaved as a young man, before he manifested his powers, but afterwards he was worshipped as a god for millennia.
Exodus went from a normal medieval european knight to minion of Apocalypse without experiencing any anti-mutant prejudice,
Magneto attacked the UN at a time nobody knew what a mutant was; he feared that mutants would be persecuted and took preventive action before actual persecution started.
Fabian Cortez, on his own admission, never experienced prejudice or persecution.
Dyscordia grew during a period when mutants ruled the world, and he was treated like a prince...
Mr. Sinister wasn't a mutant to begin with...
Yeah, other mutants went bad because of persecution, but the worst villains weren´t motivated by any form of anti-mutant prejudice...