I always wonder what the thought process is behind this. Machismo/male privilege? A lack of basic urban etiquette? An inflated sense of one’s size (the dude is big, but, at most, he “needs” two side-by-side seats)? Cultural differences (e.g., “Bah! Women are second-class humans!” or “In Gmöszk, where I am coming from, life is hard and one must prevent the wimmens, cripples, childrens, and non-Gmöszkeans from sitting down, else they grow uppitys!”)?
Personally, I ascribe it to mental deficiency. Not full-blown cognitive impairment. Just a general, dim-witted lack of perception of others, selfishness, a misplaced sense of persecution, and an allergy to acting decently because it would be “inconvenient.”
An example. I once stood up on an asses-to-elbows crowded train to give an elderly lady my seat, and a guy, about as big as this fellow and listening to his tiny electronic music box, grabbed the seat as she started to sit down. I looked at him, gobsmacked, then said: 

”Hey, buddy. I was giving the seat to this lady.”
He looked at me blankly, nodded sharply, causing his jowls to jiggle, and then said, “Oh, okay.” Nothing behind his eyes. Just marshmallow fluff.
Then he remained seated while the woman, the surrounding people, and I all stared at him. He wasn’t threatening, so I said, “Uh, hey, guy. Why not give her the seat?”
He then cleverly outwitted me by keeping his head down and ignoring us. Another gentleman two seats behind me got up and let the lady sit. I kept staring at the idiot the whole way home. He never looked up. I figured it was a combination of low intelligence, bad parenting, and, mostly, embarrassment, which always, ALWAYS fades when you continue to act like an ass. Yeah.
Mostly, these people (men) probably do it because they think most folks wouldn’t bother to confront them (not out of fear, just from a sense that it’s not worth it to mix it up with them; and then there’s the asinine/horrifying attitude that infects our country: “What if he/she has a GUN?”).
But then again… why do they do it? How does it benefit them? If you ride, say, the Blue line, from end to end, you’ll be on the train no more than 30 to 40 minutes. Unless you’re toting heavy objects, and/or you’re physically impaired, you don’t suffer much more than a minor foot cramp by scrunching into a seat.
My friend Kathy once suggested it was because they suffered from severe enlargement of the testicles. Poor souls. Let’s take up a collection.
Later Note: After reading more of the site, I’d like to add that it is hilarious to hear the “But men need to spread their legs because their junk is in the way!” Ladies, in case you were wondering, that’s a load of bollocks (chuckle, snicker). We’re not toting steel rods and bowling balls down there. They’re semi-squishable—at least enough to sit down with our knees together.