One of the (many) mistakes made by the Popular Front in the run-up to the Spanish Civil War was its decision to target Catholic churches and clergy. By 1936, Spain was well on the way to being a secular society. Mass attendance was low and falling, and there was little reason to believe the situation would change.
One of the many unique things about Francisco Franco was that he was a religious military officer, which was all but unheard of at that time. Unless it was a wedding or a funeral, Spanish men didn't go to church.
This changed when the Popular Front gained control of the Republic and its militias began a large-scale campaign of arson and murder. As Stanley G. Payne has noted, in the run-up to the war and in the chaotic months that followed its outbreak, the Spanish clergy lost a higher percentage of its members than the Orthodox Church did in Communist Russia.
With historic cathedrals in flames, it was not surprising that the surviving Church leadership agreed that it was time to fight to defend what remained of Spanish Christianity.
One could argue that this was the final straw in turning popular opinion decisively against the Republic. As I note in Long Live Death, one did not have to be a practicing Catholic to find someone burning your home parish down and killing the local priest abhorrent. Acts of desecration likewise stirred powerful - and ultimately homicidal - emotions.
This also had to have factored in the decision of the Carlist militias in Navarre to side with the Nationalists. It is important to recall that the July Rising was originally to "save the Republic." It was only later that a Nationalist ideology was developed.
The Carlists correctly reasoned that while neither side represented their interests, the annihilation of the Church was unacceptable. The Requetes from Navarre would become the true elite of the Nationalist Army, outstripping even the Spanish Foreign Legion in their tenacity and determination.
It was a self-defeating tactic, but also an inevitable one. Having decided to destroy traditional society, the Anarchists would also have to target the Church as well.
While the Orthodox Church was unable to mount much of a defense in Soviet Russia, history shows that Catholics often offer very effective resistance.