What protects the bottom of a beaker from flame

Nothing really protects the beaker. The beaker is made of glass and glass melts at very high temperatures, so a flame you use in your science class won't change the glass. Although, I have heard from my science teacher that when the bottom of the beaker is heated and cooled repeatedly, as it is in science classes, the glass might shatter after too many times of this.

What helps protect the beaker from burning is the wire mat. 

The teacher is mostly talking about the distillation of a mixture