the main reason is that "felon" lists can be very easily abused, see Florida 2000. I'd rather have every felon able to vote than have a single innocent person disbarred.
I think you mean disenfranchised. This is much less of a danger now that provisional voting is mandated in presidential elections. A person whose registration is in dispute is allowed to vote on a provisional basis until there is time for investigation, and if he/she was stricken in error from the voting rolls, the vote is counted.
I see no reason to be nice to felons. We should be stiffening penalties against them, not easing up.