it is (that) tom often breaks the school rules(that)makes his teacher unsatisfied

(that) tom often breaks the school rules这是主语从句.
(that)makes his teacher unsatisfied这个that是it is...that...强调句型的that.
这是主语从句加强调句的混合用法.主语从句什么时候用that当从句中不缺少任何成分的时候，用that引导，比如我给你觉得第一个例子，从句中主谓宾都不缺少。所以用that引导主语从句。