Different culture. People like, use, and depend on subways so they like the extensions and expect their governments to get shit done. And in Europe the power of a single individual to block major project is limited.
Well in France any hamster is basically empowered to stop a project...
While we're guessing, this may just be due to the very special environment that is Manhattan. It's been a few years since I read about it, but I seem to remember that they had to fight some quite unusual challenges, including skyscrapers, the constant influx of water, and both granite and basically liquid sediments. Manhattan probably also has an insane amount od existing, badly documented underground infrastructure.