I think there are some flaws in your presumptions. Franco's Nationalist faction did receive aid from the Nazis during the Spanish Civil War, but to call the two nations "allies" is a bit of a stretch. Franco never entered WWII on the side of the Axis (though he did allow a division of volunteers to fight for the Germans on the Eastern front for a time, the Blue Division). It is also disputed how much Franco's regime fits the "fascist" label. Along with fascists, his single party included two different types of monarchists, industrialist and large agricultural concerns, the remains of a right-to-centrist Catholic party, the military and its supporters, and other traditionalists. Given his professed affection for existing structures--particularly the military, but he also gave lip service to Catholicism and monarchism--the label of "fascist" does not apply very well.

Now, not being fascist is not really exculpatory. One of the reasons that Franco's regime faced little internal opposition was that his oppression of opponents both during the Spanish Civil War and after the Nationalists won that war was brutal. During the war, roughly 150,000 noncombatants were killed by the Nationalists for a number of "reasons." I put "reasons" in quotes because merely being an official elected under the Republic, a journalist, a doctor, a professor, a union member, or any other leftist affiliation could be a death sentence. I agree with historian Jose M. Sanchez who calls Franco's regime "barbarous."

Now, if you are asking why the US or someone else didn't oust Franco as part of WWII or after its conclusion, Franco became useful to the west as he was ardently anti-communist. With the onset and growth of the Cold War, undertaking a military effort to oust Franco would have been a difficult proposition to sell to the population of the US or UK after such a difficult struggle as the Second World War.

Internal opposition post-WWII is outside my expertise, so perhaps someone else can address that portion of your question--if that was what you were asking.

I hope that answers your question, but followup questions from OP and others are always encouraged.