Single entry only allows you to enter Egypt once, for a maximum duration of 30 days. 

Multiple entry gives you 2+ entries within the visa validity period of 90 days, with each stay being no more than 30 days.

For example, you can enter Egypt and leave after 15 days, come back and stay for another 20 days, etc...as long as each stay doesn't exceed 30 days, and all entries occur within 90 days.