The entire episode is about Homer forsaking the church and no longer attending Sunday service. When the house catches fire, the first person to get to him is Ned Flanders when everyone is at church.

Apu is the first to notice because he's a Hindu so he doesn't go to church on Sunday. Krusty is Jewish so he also doesn't go to church on Sunday. Apu likely called him and they met at the fire truck and made their way to church to pick up Chief Wiggum, Milhouse's mom, Hans Moleman, Barney and Otto with all their kit on the truck so they can be picked up and prepped on the way to the fire.

Ned Flanders was at Homer's house long before anyone else. So early in fact that he was able to get in, get homer out, then get homer out again before anyone else made it to the house. How could he do that if he was at church like almost everyone else on the volunteer fire service? This could only mean he wasn't at church. So if he wasn't at church, why wasn't he there? He's more devout that even Reverend Lovejoy and never skips Sunday service. He spent the entire episode hounding Homer to come back to church. Except on this one occasion. Where was he and what was he doing that for one single moment in his life he felt it was more important than being at church on Sunday?