The difference is that paper ballot voting can be easily introspected, whereas computers cannot. In many countries with paper ballots, the entire process from setting up the urns to counting the results is entirely done in public, usually with members of different parties being present. If you want to make sure that your vote is not tampered with, you can show up in the morning to see that the urn is empty, cast your vote, and watch the urn until it is opened in the evening and the votes are counted.