Actually the death rate for ejections is higher than you would think, and I do not remember him hitting the canopy, but it is very possible his spine was broken from twisting around in the wind etc.
Also if the pilot is not restrained in the right position the ejection could cause problems.
Another problem is when the centripital force of the spin of the plane (which I remember the plane was) is too much for the firing rockets of the canopy, it is possible for the canopy to not be ejected off properly. Although Goose's body would not have been able to move it out of the way, even though the rocket under the ejection seat is stronger.
Then of course it also depends on the type of jet and the controls. In some two-seaters the canopy is released and each pilot ejects seperately under their own control, and this could be changed by controls in the pilot's cockpit.
Either way, this is just another reason for NFS4 to hate Top Gun, an amazing movie.