Right. Without the end cap, you basically have an open standpipe. You need to cap it and drill a hole, or do what Steve said. The small hole limits the soundwaves that can escape, reducing the noice considerably.
Mike, a partial siphon will reduce the water level in the overflow box. I don't know what Rich does with his, but I personally don't like using a partial siphon, because if it becomes too strong due to fluctuations in water pull or water entering the overflow, then you can pull the water down below the input level and get the toilet sound. I prefer a hole large enough to eliminate siphon entirely, which makes the standpipe essentially an overflow system. The water level will rise to whatever point it would be if you took the cap off. If the hole I need is too big to effectively contain noise, I attach some hose and lead the sound somewhere where I can muffle it.
I have a tank set up like this. I owe someone pics of my sump system, so I will try this weekend to figure out my (gift) camera and how to post pics, then I'll post the whole thing.