This is a good question. The children's fear of Boo is rooted in the unknown. They do not know him. They have only heard stories about him, which are untrue. Based on these things, they think that he eats raw flesh and that he is a malevolent phantom. When their imaginations get the best of them, he becomes considerably worse. In other words, the fear of the unknown is powerful. This is why they are even afraid to go by his house.
When it comes to Bob Ewell, the children are not really afraid of him. In fact, they do not think of him all that much. They know that the trial was unjust, but they can do nothing about it. So, they move on. Scout and Jem are a year older and head off to school. All seems well. Therefore, Bob Ewell's attack on them is something unexpected. This is the point. The attack is so unexpected that they children do not have time to fear him.