Losing Yao for the season, the Rockets did not go out and acquire a big center to combat the long, muscular big men that the contenders all seem to have. While Hayes is a capable defender, his glaring lack of size was exposed as teams saw him for more than twenty minutes a night instead of the ten minute cameos that he managed in previous years.
A 6'6", Hayes is instantly written off by the casual fan because he gives up six inches to most centers. While he combats them with his impressive strength in the post, he does not have the skills to be a starting center in this league.
He doesn't block shots but rather takes charges, but as teams realized that they could pull up for floaters as the year went along, the need for a big athletic center became apparent. The difference with Jordan Hill over Chuck Hayes on the court was huge, and opponents drew fewer easy layups as a result.
While his gimpy knee certainly contributed to his unimpressive defensive season, it was more likely due to the extra exposure as a starting center.
Additionally, while he improved offensively, he was still fairly poor in that regard. With no post skills and a still less than can be expected layup talent, opponents could disregard him at times. While he drew a few easy layups as a result, he still was overall disappointing.
The reason he is the worst starter at center is not because he is a bad basketball player, in fact he is pretty good at what he does, defending good post players, but thrusting him into a role he is not suited for was a mistake by the Rockets management.