The father believes the dogs to be useless because they are both heavy (hard to transport on a raft) and because they eat too much while not providing any specific help. In other words, they are just creatures to be cared for, and the father is overwhelmed with having to care for his own flesh and blood.
The boys can't imagine being parted from the dogs, however. This scene underscores the importance of family, a prominent theme in the story. Family must work together and help each other. So, despite their uselessness, the dogs come ashore with the family.