Python supports both object methods and functions. Ruby only supports object methods. However, Ruby does allow you to define methods outside of an object - these become methods of the Object class. As such, any methods defined like functions become changes to all objects since they inherit from Object.
Python is also very explicit about its namespacing and imports. In Python, you should always be able to know where any name you're using is coming from. In the example from the article, 'to_yaml' is added by requiring rubygems. That isn't so apparent (in the way that 'gem' being added by requiring rubygems would be apparent). Names are reused all the time. Names sometimes aren't related to their package in an apparent way.
With Python, you have three options (one of which Python programmers will flog you for): from package import name, name2 import package from package import * -- should really only be used in an interactive python shell and not in programs
In the first one, you could then call name(something) or name2(something). BUT you can see exactly where those names are coming from -- package. Unlike to_yaml which could come from wherever, it's explicit that it comes from 'package'. In the second one, you can do package.name(something) and the like. Similarly, you can see that it comes from 'package'.
Ruby is really flexible, but I would argue that the author is correct in assessing that the ability to modify all objects implicitly is a bad thing.