Is the author of Lord Of The Flies saying human nature good or bad?

It isn't necessarily either.

Explanation:

Human nature is essentially good unless tempted by evil, the boys at first on the stranded island had their hearts set in the right place, before the role of leadership took place in the book. Humans are usually ever so motivated by self-interest, so that would mean only working together for the benefit of it all.

"Maybe there is a beast ... Maybe it's only us."

-Simon, Chapter 5