However, the official website is outdated for Rails 3.1 and not very clear either, John Nunemaker's own blog post is outdated as well and mongodb.org's Rails 3 - Getting Started is also outdated and will simply confuse you.
So, here is the quick rundown of how to start an app in Rails 3.1 using MongoMapper:
$ rails new appname --skip-active-record
Head in, edit your Gemfile and add:
gem 'mongo_mapper' gem 'bson_ext'
Do the bundle install dance, then generate your config and create a model.
$ bundle [...] $ rails g mongo_mapper:config $ rails g mongo_mapper:model MyModel
Done. You may need the initializer snippet for Passenger as shown on mongodb.org (I haven't tested it) but you won't need any of the other application.rb editing or anything.