If your project gets up to very large scale things are probably different, but there's no need to deal with that in a "Hello World"-type tutorial.
Actually, django is worse if this tutorial is correct.
http://programmingzen.com/2007/12/22/how-to-install-django-w...
They are telling you to install a binary precompiled library. I much prefer having my dependencies managed as they are in bundler than downloading libraries manually and installing them.
I know there's been some bad blood between the Ruby and Debian communities about Debian package maintainers not accepting bleeding-edge versions of Ruby software into the Debian repos; that may have been why Ruby went off and built its own set of package managers.
1. I develop on a mac and deploy on different linux distros. It makes more sense for me to have a single system for managing ruby dependencies than to do it with 3 or 4 different systems that work differently and may not be fully compatible. Plus, with bundler and rubygems I'm not stuck on whatever version the distro decides to support.
2. If I install something like the mysql driver manually or with apt-get, and then a year from now I'm no longer around and some other developer checks out the code ... how do they know which versions of the libraries were used? With bundler all versions of all gems are checked into version control. This is a big win, and they can get a system with exactly the same versions of everything with a simple 'bundle install' after a clean checkout!
Edit: 3. Also, there are likely to be C based python libraries you want to use that aren't maintained by your distro. Now you're in a situation where you are mixing multiple dependency management systems which gets ugly fast.