The biggest plus point of Homebrew according to me is that it uses out of the box OS X packages to speed up the package installation and minimizes redundant libraries. Also it provides more up-to-date packages in comparison to MacPorts, as its hosting on gitbhub helps developers to easily contribute to the project. And Yes, there is a chance of getting packages broken while updating OS.
In case of MacPorts, you will get biggest repository of packages. Apart from this, because of its loose coupling with OS X, the installed packages are less affected by OS upgrade/update.
All that said, my vote goes to Homebrew. It's a trade off that you need to consider, while choosing either MacPorts or Homebrew.
Also try out Fink, if you are badly missing apt-get. Packages are available as binaries to save the compile time. But I would not recommend it owing to its outdated binaries. You would anyway end up compiling.