The towns people blame Mr. Goodman purely based on that his car started and the he looks into the sky at night which is because he has insomnia.
Fear can make people desperate.
Charlie gets the blamed later in the story because he shot Peter van Horn. Charlie shot Pete because he thought he was a monster. It did not matter to the towns people since they were desperate to find a scapegoat.
Tommy knew what was going to happen all along! He must be the monster among us. How could he have known? Its tommy!
Fear can make people desperate When the townspeople first start to suspect that someone is not who they say they are the accuse Les. Desperate to find a scapegoat they blame him for his car starting all by itself and the fact that he has insomnia. When this cools down a bit charlie shoots Pete van Horn. Of course at the time he did not know it was him neither did any of the townspeople yet as always they where desperate to find someone to crucify. When it became so escalated that they blamed a child for merely knowing the plot of a comic book and believing it to be true. As you can see the accusations escalated with the towns panic and range from in the beginning a car starting to a dead person to the accusation of a child. Fear makes you do crazy things.