Look, of course there are going to be similarities. For crying out loud, a monster knocks down a skyscraper, we see it collapsing, then the huge dust cloud coming at people. We all know now what happens when skyscrapers fall down. Are we suppose to not show it in a giant monster movie because it reminds us of 9/11? If they didn't show the dust cloud, people would say it looked fake because we now KNOW what it is like in real life.
I will say however that the plot(yes, there is one and it is good because we get character developement along with great acting), could evoke the fears of 9/11 but what is wrong with that? Something anfathomable is happening, just as on 9/11 and it shows how a small group of people deal with it. And just as on 9/11, when you think this nightmare can't get worse, it does(and is just as unbelievable). And the deep beauty of this movie is you see people being human and in turn doing their best to be the best they can to each other, as well as making me think "jesus, what the hell would I do." Abrams said he wanted to make America's own Godzilla. Well, Japans Godzilla came about because of the fears and after affects of the atom bomb. And it could be said that this movie came about by the fears of global warming and terrorism. Its actually making a statement more than "here's a new monster movie". I think this is why some have hated the movie because they were expecting a michael bay action flick and one where they don't have to think too much about what is really going on. The more I get others thoughts on what was going on and the more I think about it myself, I really think he has made a classic movie. Its not perfect, but he did succeed in making a thinking mans monster movie.