John Wender is suspicious of David because his father is Joseph Strorm, the head of their religion.

John Wender is Sophie’s father.  He has good reason to try to protect Sophie.  She is not like everyone else, in a world where not being like everyone else is very dangerous indeed.

We had an unspoken understanding that we were on a man to man basis. It had always been like that. When he first saw me he had looked at me in a way that had scared me and made me afraid to speak in his presence. (Ch. 3)

David Strorm’s father is no joke.  He is a tyrant.  David shares a story to demonstrate this.  He cut himself one day and accidentally wished for one hand.  To say that his father overrated is an understatement.

“Were you, or were you not, expressing dissatisfaction with the form of the body God gave you – the form in His own image? … You blasphemed, boy. You found fault with the Norm. Everybody here heard you. …” (Ch. 3)

In Waknuk, it is not acceptable to be different in any way.  You must all look exactly like the “True Image” (which they seem to have determined) of God, and anyone who does not is a mutant and must be destroyed or cast off.  If it is an animal or crop they destroy it, and if it is a person, they sterilize the person and send him or her off into the Fringes and then Badlands.

This is why Sophie’s dad has to be suspicious of David.  He has to protect his little girl, because she has extra toes!  A normal person has five, and Sophie has six.  This makes her in constant danger.  David saw this one day, and did not turn her in.  Instead he befriended her.  However, John Wender was still cautious, because a father has to protect his daughter.

Even if David would never intentionally turn Sophie in to his father, her having David for a friend was still dangerous.  Actually, her having any friends was dangerous.  As you can tell from the quote from David's father, this society was a dangerous one ruled by a fanatic.  Fanaticism is a danger to anyone who is different, and Sophie was always at risk.