Here, when we say "je n'en veux plus", we actually use the phrase "vouloir de quelque chose" and not "vouloir quelque chose".
"Vouloir de quelque chose" means, in this context, that you don't want to keep something any more.
So :
je ne le veux plus = I don't want it anymore;
je n'en veux plus = I don't want it anymore in the sense of I don't want to keep it anymore, for example because you don't have any need of it anymore.
"Vouloir de quelque chose" can also mean that you accept something.
These two meanings are the most common ones. Note that they are usually used in the negative form to mean "not to want to keep something anymore" or "to accept something". Example for the latter : je ne veux pas de cet argent = I don't want that money in the sense of I won't accept that money, for example because it's black money.