Preferring a paper-based system is your prerogative, that goes without saying. For what it's worth, I'm also partial to the manual system for its robustness.

However, the Estonian governement has made a different choice and I salute that they are at least trying to do everything by the book and in the right way. Publishing the source code is a part of that. Estonia is a high-trust society (which is an incredible achievement in itself, considering they were a province of the Soviet Union only forty years ago) and they have the most functional e-identity system in the World. Voting is just a part of it. It does make many things easier and also helps economy if you can trust - and verify - your fellow man.