No, the problem is exactly that the male faculty are friends with the male student, and the male student receives extra benefits from that friendship that the other students do not. This thread is not about discrimination against the female students, it is about the favoritism toward the male student. The favoritism here is gender based, but it could have been easily been based on race, religion, sexual orientation, marital status, or the faculty and the favorite student all being underwater basket weaving enthusiasts. Many people (myself included) believe favoritism in any form is unethical, but there are still significant numbers of people who see no problem with it or even openly practice it as if it were a virtue.
Favoritism in any setting breeds resentment, frustration and anger among the unfavored, and sometimes even hopelessness and despair. It gives the favored a sense of entitlement to the inequitable allocations of benefits and a lack of appreciation for the advantages they have received that others have not. It also sets up the favored as a potential target for retribution or sabotage. It encourages conflict, breaks down teams, and prevents work from getting done. Favoritism allows the talents, knowledge, and abilities of the unfavored to go unrecognized, unrewarded, and wasted, instead of being put to effective and meaningful use. Favoritism is usually only seen or sensed by the unfavored, seldom noticed by the favored, and routinely denied by those who practice it (although some will boast about it). Those who practice favoritism, whether consciously or unconsciously, eventually lose the trust and respect of the unfavored and anyone else who can see the favoritism and does not agree with it.
Eigen, I've seen you give good advice in many other threads, but I, for one, do not take any of your advice or statements in this thread seriously... not because you are male, but because you have clearly stated that you choose to show your male students favoritism and will continue to do so. You choose to perpetuate those double standards. The reason why does not matter to anyone but you, because your actions are what make a difference (or not) in your students' lives. Your female students have no choice but to do without, while watching the males reap the benefits you give them. The reason there are those gender-specific support groups is because that outside of those support groups, there are many, many people who think like you do, who are in positions of authority and can grant resources and opportunities as they see fit, and who view themselves as supporting women, even while continuing to give advantages to men and justifying it in ways like you have written above. You are frustrated that you are not viewed as an ally -- why should you be, when you choose not treat your students equally? (Rhetorical question. Only you need to know the honest answer to that.)
Seriously: you cannot show favoritism to men and expect women to believe that you will have their back. Maybe I've been harsh in my statements, but it's because women live with the much harsher reality of favoritism every day. Because favoritism is the root of why there are not more women and other underrepresented groups in STEM fields, not any of the other excuses that people think can be fixed with school outreach programs and whatnot. Because favoritism promotes the success of the favored through greater assistance and opportunities (even simple things like a prof giving you temporary lodging), and the unfavored move on to other areas in search of receiving the same opportunities as everyone else. Unfortunately, many never do get those opportunities.
I really didn't intend this post to be so long and preachy, but I thought someone had to say this. Not that it will actually change anyone's behavior or point of view -- I gave up trying to do that a long time ago -- but at least Pscott and others going through similar experiences can know that some stranger on the internet believes them and understands how damaging these situations are to all involved.