A flat spin is a special circumstance which can, in some cases, increase the risk of impacting the canopy. In a flat spin in the Tomcat, the pilot does, as Maverick is depicted, end up pinned forward. As a result, it is up to the RIO to ensure the canopy is safely out of the aircraft's airflow to ensure survival before initiating the final ejection procedure. From what I understand, this specific danger is addressed in the 'F-14 Out-Of-Control flight procedures,' in which the second to last step is 'canopy - jettison.' This involves the separate action of pulling the handle that jettisons the canopy, independent of any ejection. In other words, only then, after the canopy has had time to separate, do you initiate the ejection sequence.
The special edition features of the Top Gun DVD make mention of this as well. The pilot consultant, who was himself a Top Gun instructor (IIRC), created this sequence based on actual aircraft incident reports.
Thinking logically about it, it does seem reasonable to assume that the canopy could get held in an area of low pressure above the aircraft that is essentially falling straight down.
Now, where things get dicey is the fact that technically speaking, the ejection seats should offer some support in the way of absorbing at least a portion of the energy from the hit were the operator to actually launch himself through the canopy.
Of course, my information could be completely out of date, and this data probably varies wildly depending on the type of aircraft. Nevertheless, it would appear that Goose probably should have stuck to singing "Great Balls of Fire."