The skipper has many pros, one of the many, and probably the most important, is that he is a good sailor. If he wouldn't have been a good sailor, the guys would probably would have died, starved to death, or gotten lost in the middle of the ocean. He is very good at his job, he keeps all the young men in order and disciplined to an extent, he did however, lose 5 of his crewmen in a huge storm. When himself and his crewmates are rescued and return to land, he is blamed for everything that was bad that happened on his ship. Just think if the sailor would have been a bad sailor. They, without a doubt, would have been dead or killed within a few weeks or earlier depending on the sea conditions.
The skipper also has an ability to persuade people to face their fears. This may not sound like a very good attribute, but as it turns out this actually comes in handy later in the movie. An example of this is when one of the men needed to rescue another crew mate. If the skipper never made him climb the ladder, he never would have learned to face any more of his fears in life. This movie was based on facing your worst fear and beating it.
The third and final reason stated is that the skipper is a great leader. If it weren't for his great leader skills, all of the crew would be disorganized and much undisciplined. If this were true he would have no control whatsoever over his mates. The skipper seemed to have an uncanny knack for leadership that made him the best leader suited for this voyage. When the white squall hit the ship, he stayed calm and never panicked once, and that resembles a great chief in command.