Ejection isn't a get out of jail free card. I've heard it described as being just barely preferable to crashing. There's a decent chance of significant injury and even death in an ejection.
I recall seeing someone run the numbers, and it turns out that the guy in your link had it worse, as the much lower altitude more than made up for the lower speed.
An ejection seat is actually only slightly safer than crashing the plane; the strain it puts on the vertebrae in particular is enough to force the pilot to retire after a few ejections.
And it sounds like he was flying over water, which carries substantial risks in itself.
Living on a fighter base, I met two people who were forced to eject from a plane. One lost 2" of height due to severe back/spine compression, one bounced off the ground so hard he could never fly again due to leg and hip issues.
Not to mention, an ejected plane can now go hit some school or office building, whatever causing all sort of casualties. Most pilots would rather just try and survive the crash and risk their own life.
There's a typical trend of people underestimating the severity of dangerous situations, but also pilot bravado in thinking, "I've got five minutes of altitude left, I can save this thing!" rather than the desk jockey, hindsight view of "He's only got five minutes to live."
Pilots want to retain their control, and even a damaged plane can usually be controlled. Plus - surprisingly - many pilots claim to be afraid of heights, and cite this as a reason they'd rather not eject. And, of course, ejecting is no guarantee.
