The most common and most likely answer to this crossword clue is the 4 plus 4 letter word LEAD ROOF
I've seen this crossword clue in The Guardian
L
E
A
D
R
O
O
F
Buddy explains!
The straight part
We know that "what protects many churches" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case what protects many churches = lead roof.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.