With Fabric you tell what to _do_ and with Puppet/Chef you define what the result should _look_ like.
You define how a server should look like and it can make sure its true for 1000 servers. Or 10000.
It’s not about Fabric vs. Puppet, but how to use both in the most efficient way.
I prefer to deploy applications in the home directory of a dedicated user account with minimal privileges, and use fabric for installing updates and running application tasks.
OTOH, I'd prefer to be using puppet for creating the user accounts, managing the installation and configuration of PostgreSQL, putting app configuration in a safe location, and so on.
This comes down to my (maybe antiquated?) view of having multiple applications running on a single server.
Maybe I should add a “running apps as root” anti-pattern, but this its 2012 after all, everyone should know that, right? :-/