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.
And it sounds like he was flying over water, which carries substantial risks in itself.