That article makes a few too many assumptions. While the overall premise is accurate, I think the author digs a little too deep in an effort to find feminism at every turn.
In particular, I was never under the impression that the cube was a male entity. The author suggests that man is the default loving (hearts) 'companion' to woman, but since the cube was completely inanimate, it's just as easy to assume that the cube is 'mother', 'sister' or 'daughter', especially since the game puts so little emphasis on the sex of the protagonist.
Given what's been written of Portal's back story, (GLadOS malfunctioned years ago on bring-your-daughter-to-work day) I tend to think that the cube is meant to be either a playmate or a parent, not a sexual partner.
Also, while GLaDOS may "come to represent man's attempt to construct an idealized mother figure through the cold logic of science", I feel I should note that GLaDOS wasn't programmed to be a mother figure. As I understand it GLaDOS is simply trying to mimic what she's seen of human parenting (bring-your-daughter-to-work day) in an effort to control her test subjects - the cake is the most obvious example.
As for portals representing female sex organs, I'll leave that one alone.
