Because WWII was never waged as an ideological war against fascism.

Franco was a pragmatist par excellence, and was very careful to steer a course in between the Allies and the Axis for more or less the entire duration of the war, never committing to either. He did this of course, for precisely the reason that he did not wish to be overthrown should he find himself on the losing side, despite his personal sympathies with the Axis (especially considering that he likely would never have been able to defeat the Republic without the aid from Italy and Germany).

Franco had, during the high-water mark of Axis success, shifted Spain into a position of 'co-belligerence' and seriously considered entering the war. Official state press was intensely sympathetic towards Germany. U-Boats refueled in Spanish ports. Franco's brother in law Serrano Suñer, a committed Fascist and Germanophile, served as foreign minister during this time. But Franco was ever careful and unwilling to commit, and soon enough, Germany's fortunes took a turn for the worst, and he soon distanced himself from the fascist powers.

In short, by the end of the war, there was really no pretext for overthrowing Franco. He had never fought alongside the Axis officially. He had never declared open opposition to the Allies. The populations of the Allied countries were exhausted by the war. It would have been unjustifiable to invade a neutral country, and cause thousands more deaths, simply because its government had fascist sympathies. There simply was no reason to cause more turmoil in Europe.

Of course, it's worth noting that many Spanish Republican exiles (and Republicans in Spain) had hoped the Allies would do precisely that. Indeed, for a few years after WWII, Franco's Spain did become an international pariah of sorts. The UN passed a resolution condemning Spain's form of government as fascist and the country itself was barred from UN membership.

But once WWII ended and the Cold War began, Franco's staunch anti-communism soon became usefull to the United States and its allies in their fight against the USSR. Spain became the recipient of western aid, and Franco framed the Civil War as a crusade against Bolshevism in which he had only accepted the aid of fascist powers because they where the only ones offering. He soon styled himself the 'Sentinel of the West', the first to have fought against the scourge of communism.

And that was that.