The magnetite Jeffrey Spender had injected him with didn’t take away his special abilities, and William’s adoptive parents simply weren’t equipped for the weirdness of a son with powers.
By all accounts, his adoptive parents loved him and took care of him, but they didn’t have years of experience with the paranormal.
If he had been raised by Mulder and Scully — who are probably more used to weirdness than they are normal life at this point — he likely wouldn’t have had to struggle as much with his abilities.
As much as Scully gave William up in the hopes of allowing him to have a normal life without shadowy government figures, aliens, fanatics, and/or super soldiers constantly turning up on his doorstep, she couldn’t stop him from developing powers.