On the most basic level, Salem's House is a pretty awful school while Dr. Strong's school is a fine school.
Salem's House essentially treats its pupils like inmates at a prison. The master takes pleasure in using corporal punishment on the students, not because he thinks it will make them better people, but because he relishes the power he has over them. As the other answer mentions, the very building and its rooms are poorly maintained and dreary.
That Mr. Murdstone sends David to this school is telling. The school reflects Murdstone's cruelty and uncharitable view of David's character. He does not believe in nurturing children so much as ensuring their blind submission through any means necessary.
In contrast, the Canterbury school treats its students with respect and does not assume they are evil little beings who need to have proper education beaten into them. It is assumed that students are at heart not bad people and this inspires the students to do their best generally. The building itself is neat, clean, and dignified.
Dr. Strong himself is an honorable, reliable man and he inspires his students to cultivate these qualities in themselves. He is the good father figure to the tyrannical models represented by Murdstone and Mr. Creakle.