While the meaning of "something simple" is, well, simple, "not quite so simple" means, in reality, something requiring a detailed explanation. This expression is used to alter the flow of a conversation or, more usually, an article, shifting to an explanation which explains why a question cannot be answered simply and reflexively.
Example: "When faced with a wild bear, what should one do? Scream? Run in panic? It isn't quite that simple. Either of these reactions may trigger the bear's predatory instincts and place the person in greater danger..."