Quite simply because there was no reason to overthrow him.

WWII was not a crusade against fascism waged on ideological grounds. Italy and Germany fell because they pursued a war of aggression against the rest of Europe. Franco was smart enough to keep his country out of the war (if he had not, he almost would have been toppled as well, in '45 or earlier).

The Spanish Civil War was viewed abroad by many unsympathetic towards the left as a war between tradition and order on one hand and godless bolshevism on the other. This led to quite a bit of support for Franco and his cause in the western democracies, particularly among the moneyed classes, who naturally exerted a powerful influence over their governments. France and Britain immediately recognized Franco's government when the war concluded.

So by the time WWII rolled around Franco had by and large been recognized as the legitimate, if often unpopular, ruler of Spain by the international community. Seeing as he did not enter the war on the Axis side (despite his and his government's strong sympathy), there would have been no real pretext to overthrow him. It would simply have been an aggressive war waged upon a government already recognized as legitimate by most world powers.

As soon as it became clear the Axis would be defeated, Franco began to disassociate himself and his movement from fascism. The roman salute lost its official status, the fervently pro-German foreign minister Serrano Suñer lost his post, and the 'Blue Division' of volunteers fighting with the Wehrmacht against the USSR was recalled.

Thus, though Spain remained something of an international pariah during the immediate post-war period (the UN, I believe, passed a resolution condemning Franco's state as a fascist one), it slowly distanced itself from Hitler's Germany and Mussolini's Italy, and thus became a country other respectable powers could 'do business' with again.

Of course, with the Cold War swinging into gear, Franco's fervent anti-communism gave him an in with the US and its bloc. Spain thus made herself useful, and the Madrid Pact signed with the US in the early 50s codified this alliance, allowing for US bases in Spain and shipment of aid from America.

Short version: Franco did not pursue an aggressive foreign policy that could justify his overthrow in the eyes of the international community, and in later years his strong right-wing stance made him a valuable anti-Soviet ally.