There are some interesting thoughts in this video. I haven’t played all of the Final Fantasy games, but fighting gods or god-like beings is pretty common in the ones I have. In some ways, I don’t think it’s necessarily anti-religious so much as it is just wanting to pit your characters against the most powerful enemy they can think of, and what’s more powerful than a god? Also, in FF6, you have to remember that Kekfa usurped the power of the three goddesses in order to gain power, so you can certainly argue he’s more of a Satan figure (i.e., wanting to overthrow the power of God) than a god in his own right.
Of course, the fact that the goddesses could be overthrown so easily doesn’t exactly put much faith in religion, and I don’t recall that game having a supreme being as such. This can apply to a lot of arch-villains in both FF games and others. I haven’t played Final Fantasy Legend, but it kind of strikes me from what the video shows that the main enemy is more a parody of the creators of the game itself than of God the Creator, although there’s no reason he can’t be both.
And the religious figures and symbols throughout the games aren’t always bad. Holy spells can be used for good, and summoned beings include gods from various cultures.
I also want to point out Breath of Fire II as a game where the entire church structure is only giving more power to a demon. Again, he’s not a true god in the sense we would generally think of the term, but it still strikes me as a critique on organized religion.
The game also has the Dragon God, who’s good but not all-powerful. The Zelda series shows a world created and maintained by goddesses, which could be interpreted as a positive portrayal of polytheism.
Dragon Quest games usually present God (or the Goddess in some installments) as good and powerful, but not always involved in day-to-day events. In fact, in DQ7, part of the game involves resurrecting God.