I think part of this can be ascribed to how the West and particularly Britain viewed Portugal during the war years.

At the start of WWII Salazar explicitly announced that the Anglo-Portuguese alliance was still in effect. But according to Portuguese statements as long as London didn't call for aid, Lisbon was allowed to remain neutral. Five days later London issued a memorandum confirming that understanding. It was felt that if Portugal were to join the allies it would drive Franco into Hitler's arms. So by keeping Portugal neutral, they hoped to keep all of Iberia neutral. In 1943 the situation had changed somewhat and the British invoked the alliance treaty and requested bases in the Azores. Salazar quickly approved the request and opened Azores ports and airfields to allied military craft.

Basically Spain was viewed as an unfriendly country that it was important to keep neutral, while Portugal was viewed as a friendly country that it was important to keep neutral. The fact that Salazar did jump the one time the allies asked him to greatly enhanced that reputation.

In addition Portugal didn't exactly play nice with Hitler. They accepted Jewish (and other) refugees throughout the war. Due to the geography of the war, that largely meant they accepted refugees from areas occupied or threatened by Germany. Also unlike other countries, Germany wasn't able to recruit many Portuguese men into their foreign divisions. While Spain provided roughly 500,000 soldiers to Germany, Portugal provided 159. And almost all of them were men who had fought in the Spanish Civil War.

So when the war ended Salazar was seen as a friend. Franco was seen as something more like an enemy who wasn't worth going after. The fine line between Salazar and Franco had a lot more to do with Salazar being "our" man (according to the British) than any real significant differences in governments.