I don't think there is any benefit in arguing that rape is worse for men than for women, or the other way round. It's similar to arguing that rape is inherently worse for "some" women (e.g. virgins, those who've had few partners, where perpetrator is a stranger, where they are seriously injured, etc.) than for others.
I've been close to both women and men who've been raped, as adults and as children. I know the plural of anecdote is not data, but there are so many factors in a person's life, personality, situation and facts related to the incident that influence how they cope with what has happened. Stating that gender or any other factor governs how "bad" a rape is is deeply offensive, does little to help those who've been raped deal with what's happened and adds nothing useful to public discourse on rape.
I agree that in that article at least there seems to be a misogynist undercurrent that women are "used" to having sex "done to them" and because rape is an extreme version of that, it has to be worse for a bloke who's not used to it. It's what I'd call "casual misogyny" - taking something that is deeply sexist for granted as something that just "is" rather than something that is founded on the validation of a form of oppression as normal or natural.
This kind of reminded me of the plethora of debates I was once involved in with the precursors of MRAs. They insisted that partner abuse was more common and worse for men than it was for women and it was wrong that there was Women's Aid and other organisations to support women but nothing like that for men.
Apart from the fact that there were services, but different types (as it had been found that men leaving abusive relationships didn't need or want refuge space,) I would think if you were genuinely concerned about the welfare of a group of people who were being abused within a trusting relationship, the last thing you'd want to do is try and get rid of services to support another group of people suffering the same plight. You'd want to stand shoulder to shoulder with those who'd campaigned for services for women and insist on MORE services for victims (including men) and not cutting the already overstretched and inadequate services for men.
That sort of busted what their real agenda was about - not helping men, but taking down women. Yep, this article reminded me of that.