I tried your project and it appears to be working fine.
What I have done in the past is run pub build and hit the built file in dartium and that will not work. So you have to hit the build file from chrome proper. So if I load .../mathlets/build/web/mathlets.html in chrome it works fine.
The reason for this is because pub build is the release build, which does not copy any of the dart files. However the index file still has the check if dart is enabled than try to use dart files. Well in dartium dart is enabled but the build doesn't have the dart files. In chrome dart is not enabled so then that 'packages/browser/dart.js' file dynamically writes the mathletes.dart.js to index and launches the app that way.
If you want to work around this and improve performance of the release build at the same time you can use this transformer: http://pub.dartlang.org/packages/dart_to_js_script_rewriter
We are using this also. Ensure it's the last transformer run though, if it's before the angular transformer there are problems.