Well obviously none of us can know for sure one way or the other, or even if this was a protest at all. But what do you hope the outcome to be? If they did some sort of investigation and found out the pairing algorithm was rigged to favor women-women matchups, that would be crazy. I love a good conspiracy-turned-out-to-be-true story. What if it's been rigged all along to favor certain players and help them get to the top? Doubtful but would make for one interesting documentary in the future.
Hou Yifan plays the Fool's mate. Resigns after move 5 in 2017 Gibraltar Masters.

In the video, the organizer of the tournament clearly states that the pairings were generated by a machine and that there was no human intervention.
There's no way for him to be sure of that. He's a guy who provides money, not the IA who did pairings. And even so, Yifan is claiming the opposite. The way to find out would be to analyze the pairings.
It seems both the pairing program and tournament file are available to download
http://www.chess-results.com/tnr257693.aspx?lan=1&art=4&turdet=YES&wi=984
http://swiss-manager.at/download.aspx?lan=1

In the video, the organizer of the tournament clearly states that the pairings were generated by a machine and that there was no human intervention.
I watched that and it is a bit of a cop-out I think. I've never paired with whatever they were using (because I'm sure it wasn't WinTD or Vega) but there are usually options, as mentioned in post 43, that could potentially set in such a way to cause pairing issues and those may or may not be correctly set. So, the reasons may still have been caused by human error.

"I don't see the reason to pair her against other women on purpose."
It's done nonetheless. Not just in this tournament. For most women is okay, or at least they don't complain. But for Hou Yifan it becomes a problem, as she was playing Pia Cramling one day, and Michael Adams the other, making it harder to keep the same level of play as the challenge is too different.
She had 3.5/4 and was paired against Adams who also had 3.5/4. Yifan lost and was then paired against Cramling who had 3.5/5 I don't see why that's a problem.

Human intervention is always involved. Someone has to write the code and the algorithm for pairing.
These programs are usually widely used, not some unknown personal program one of the IAs brings with them.
But yeah, as some have pointed out, these programs have options to change pairings... at least the programs I've used for USCF do, and I can't imagine not having certain options so I imagine it's the same way for FIDE. That said, whether or not the pairings were manipulated or against FIDE rules is not known. It could just be coincidence that many of her opponents were female.

I find it more concerning that she has to sit in the front of a door where people stumble over her every second... So much prize money but not enough space for the players?

A 2650 GM who thinks she's special when she's just an average GM that wants people to pay attention to her...

It is necessary that if one player is paired with a lot of female players, and female players are a small minority, that no other player will have as many female opponents. That other players with a similar point progression didn't play as many female opponents doesn't make Yifan's pairings more or less suspicious.

"I don't see the reason to pair her against other women on purpose."
It's done nonetheless. Not just in this tournament. For most women is okay, or at least they don't complain. But for Hou Yifan it becomes a problem, as she was playing Pia Cramling one day, and Michael Adams the other, making it harder to keep the same level of play as the challenge is too different.
She had 3.5/4 and was paired against Adams who also had 3.5/4. Yifan lost and was then paired against Cramling who had 3.5/5 I don't see why that's a problem.
You can also check whom she was playing before the game with Adams.
Maybe this isn't that clear for some. Those at +2650, who are about to face +2700s, get no real benefit playing 2400–2500s.
It's an Open, you know. Caruana has +2800 elo and he has faced two 2300s, one 2400s and three 2500s. Yifan is just behaving in an idiotic way because she wants to be the center of attention.

"I don't see the reason to pair her against other women on purpose."
It's done nonetheless. Not just in this tournament. For most women is okay, or at least they don't complain. But for Hou Yifan it becomes a problem, as she was playing Pia Cramling one day, and Michael Adams the other, making it harder to keep the same level of play as the challenge is too different.
She had 3.5/4 and was paired against Adams who also had 3.5/4. Yifan lost and was then paired against Cramling who had 3.5/5 I don't see why that's a problem.
You can also check whom she was playing before the game with Adams.
Maybe this isn't that clear for some. Those at +2650, who are about to face +2700s, get no real benefit playing 2400–2500s.
It's a large open, so being paired with Adams after a 2500 is not noteworthy. By the way her opponent before Adams, Muzychuk, is rated only 98 points below her. It's not like it was effectively a bye where she didn't have to concentrate. Of course the first few rounds all the strong GMs are playing non GMs. Caruana played a 2300 in round 3 then a 2600 in round 4.

It's an Open, you know. Caruana has +2800 elo and he has faced two 2300s, one 2400s and three 2500s. Yifan is just behaving in an idiotic way because she wants to be the center of attention.
Agreed. She has probably noticed that she is not as famous as she would like to be
In the video, the organizer of the tournament clearly states that the pairings were generated by a machine and that there was no human intervention.