It means that the vibe of the church have him a sense of foreboding, meaning he could feel something bad was about to happen. Spiderwebs just add to the creepiness, making him feel uncomfortable in the church.
I loved both the book and movie of the Outsiders ;w;
Answer: When Ponyboy and Johnny first approach the church, Ponyboy feels that it's a creepy place, and he has a sense that something bad will happen there. He repeatedly describes it as an old, spiderwebby place that makes him feel scared.
