Yeah - It does sort of suck. The NY skyline is highly romanticized, it's hard to imagine it any differently. The thing is, if it's going to be rebuilt, there are a few really good reasons to change it.
One - obviously, it would be a clear target if anything like this should be attempted again in the future.
Two - The skyline, going back to the way it was, would make some people feel like the builders were trying to gloss over what happened, and no one should ever forget those who died in this tragedy. The absence of those towers in the skyline will remind everyone of this event forever.
Three - they're being rebuilt, so it's not like the terrorists are winning any victory over this. The towers will be re-erected, only different. Better, if you think about it. They're housing some of the most highly protected office space in America. It will be an even more secure location than it was.