Two themes are A) Intelligence isn't everything, and B) true friends should accept you the way you are.
Explanation:
In Flowers for Algernon, you'll notice that the main character is... different from his peers. By noticing that, you will also see the fact that his so called "friends" will also make fun of him for that (and put him in some unsavory situations), which only supports the point I'm attempting to make. Furthermore, another theme in the book is that intelligence isn't everything,  which is reinforced by the ending of the book itself, when the main character gives up the intelligence for his own health. Hope this helps! :)