While both regimes shared very similar outlooks (Corporatist, authoritarian, conservative, anti-communist states) both had significantly different reputations after the 2nd world war. Salazar was an incredibly well regarded statesman, who had a great dislike for Hitler and who stayed neutral during the war due to a strategic issue (Anglo-Portugese alliance stayed intact as a strategic issue, as Portugal was poorly defended and the British did not need more reason to draw the Spanish into the war.) Franco had presided over an incredibly bloody civil war and had only stayed neutral in the 2nd world war because the Germans thought his conditions for Spanish military help were unfeasible (Rumor is Hitler once stated he'd rather have teeth pulled than continue to deal with Franco).

Four years after the end of the 2nd world war, when the North Atlantic treaty was signed, few people had forgotten had close Spain was to becoming a full-fledged member of the Axis.

Follow-up question: Could it be related to the perceived relevance of the Lajes Airbase (Azores) as a refueling point and strategic position in the North Atlantic region? Also, if anybody cares to weight in, how much relevant was this airbase really in the Cold War?