Ok, so here's my thought on it.
While I never did play the game (Didn't even know it existed), it actually did make sense to remove it.
Now just because something gets removed doesn't mean that Tom is trying to limit the creativity of people. He's trying to make sure this site isn't destroyed like who knows how many sites. If I had to choose killing someone in order to prevent the deaths of millions, I would do it. He had to remove the flash in order to save the millions of flash movies and flash games that are on this site.
Now, I'm not saying that I personally know Tom. (I only know he runs Newgrounds and that's it) But I think he views Newgrounds as one of his own children. It's important to him in a way I would probably never understand unless I also ran a site that existed before the year 2000 (Not a lot of sites can claim this.)
If he has to do something in order to prevent this site from being removed from the internet, I wouldn't hold it against him. It's his site. I'm not gonna tell him what he can or can't do with his site.
For those of you saying that this was a bad move, put yourself in his position. Pretend to be Tom Fulp, and you have been running a site JUST like his. You have a flash game and movie site that's been around since 1999. It is the year 2013, where everyone will be offended and try to put you in jail for saying the word piss in public. Then comes along a flash game that is based on a tragic, terrible event that happened. You have two choices.
1. Let this game stay. You will get quite a lot of attention. But every single ad service leaves your site, resulting in that eventually, you will no longer be able to pay for a site the size of Newgrounds. Years of work made by who knows how many people are destroyed. Most likely, they won't be put back up.
2. Remove the game. People will get pissed over this. But it would ensure that your site would still have some ad services, allowing the site to exist FAR longer than it would have should the game remained. Years of Flash games and animations get to remain. However, doing so would basically violate what the site stood for.
Tom had a hard choice. Let his site get removed over a game to stay with the idea of unrestricted creativity so that he wouldn't violate what it stood for, or keep the site that he has owned for over a decade, but violate what it stood for.
This was a no win situation, no matter what he does. Again, I'm not saying I know him, but if he had let the game stay on and the result was that the site got removed, it would probably destroy the man.
He also did something that not a lot of people seem to do these days: He gave a shit about someone other than himself and he gave a shit about the feelings of the parents of the kids killed in Sandy Hook Elementary, even though it was at his own expense. It means he's still HUMAN, not some emotionless robot that people seem to be turning into.
While trying to send a message is a good thing, there are a lot of ways that it can be done wrong. This was one of the wrong ways.
It's not the end of the world if a Flash game or movie is removed. There's still like....a MILLION to choose from, some of which are probably more violent (Like the Madness Series) or offensive (Like the stuff Sexual Lobster makes.)
As for those saying that Tom is a greedy bastard or some shit like that, He NEEDS the revenue. Nothing is free. For fuck's sake, not even water is free. Sites cost money to run. I'm not sure why, but it just does. No money means no site. No site means no Newgrounds. No Newgrounds means no Madness Day, Robot Day, Pico Day, and any other day's I can't think of. If there's no Newgrounds, then there's no Madness Combat or any of the millions of flash series out there. Let me tell you something. There is nothing worse that can happen to something than to be forgotten. That's probably what would happen if Newgrounds got shutdown.
And it wouldn't stop there. Newgrounds allows artists to post their main sites on their user page. What would happen if that link disappeared. It would affect a LOT of people...in a bad way.
Anyway...It was a tough decision to make, But I think Tom had no choice but to remove it.