Times were much simpler in 90's America
Another reason for its decline in popularity is that the issues it takes on are a bit dated. Back then, homosexuality and marijuana were taboo and now both of those things are commonly accepted.
Times were much simpler in 90's America: a.k.a. just the usual. "Less materialism; more love" was the answer to most problems then so American Beauty resonated. Now, there's the economy, debt, war, ISIS and so on.