I had heard that Capra supported General Franco. Doesn't sound like a lifelong apathy towards Catholicism.
Did he "support" them, with money and influence, or did he "root" for them? There's a difference.
At that time, there were also more obvious reasons to root for Franco than the fact that the Catholic Church in Spain was on Franco's side against the communists. In Capra case, it was most likely because he was such a vocal opponent of FDR and the New Deal.