There are too many potential vulnerabilities and uncertainties involved in using a complex electronic system. Quite apart from issues of tampering and vote rigging, there are possibilities of programming errors going undetected.
It is very difficult to tamper with a piece of paper marked with a pencil. Even using a pen adds extra variables (like people replacing the pen with one that uses disappearing ink - it has happened!). For an issue as sensitive as voting, we should remove uncertainty as much as possible.