As the article notes, they've tried this before and the algorithmically generated route map didn't work well in real life. Assuming the algorithm was good, the issue was probably that it didn't incorporate significant real-life factors.
Perhaps they are getting more sophisticated though, by having the people who have been doing this work by hand review the results and make adjustments (as the article says, e.g., at first the algorithm allowed big busses on narrow streets, which apparently doesn't work well).
Speaking of the people who have been doing the route maps manually... they seem to have been doing an impressive job since the algorithm is expected to be only 4% better.