We still don't know. A lot of people are saying that it was more faithful to the book, but the ending in the script that I read was:
[blackout]When the creatures get into the house, Neville can't find Anna and Ethan in time so he has to retreat down to the lab, like in the movie. He then puts on a quasi-last stand and takes a bunch of them out with machine gun and pistol fire as they bottle neck in the door. Eventually, the "Alpha" creature walks through, holding Ethan and Anna by the necks. He motions toward the female creature that was strapped down to the operating table. Neville gives the female creature to Alpha, and Neville gets Ethan and Anna back. Neville then goes through the whole "I can save you. I can fix this," speech. The creatures don't seem to care, but they do start to retreat. Alpha turns away and begins to walk away, but Neville grabs him and throws him to the ground, and proceeds to beat the bloody pulp out of it as he keeps saying "let me save you."
It then picks up the next morning. Neville, Anna, and Ethan are all in an SUV, they all drive over a bridge (In the script, it was revealed that one bridge was left standing as a last resort type deal. That was how Anna and Ethan got into Manhattan. I don't remember what bridge it was.) as they go toward Vermont. In V.O. we hear another radio message like we heard earlier, but this time it's Anna laving the message. I don't remember what it said though.
My primary computer, which has the script saved onto it, is getting fixed, but when I get it back, I can transcribe sections and verify this stuff. It's been months since I read the script, so I don't 100% remember the details, but that was about the gist of it.
Also, they seemed to have cut out an entire section of the script that takes place between the time that Neville does the whole Shrek scene with Ethan and the time that they're attacked. There's a good 10-20 pages where Neville takes them out into the city, where they get a whole lot of exposition and stuff done. You actually learn about what else happened in the world and what happened to Anna an Ethan leading up to the time that we finally see them. I know at least some of this was filmed because I saw some f it being filmed on a little blurb on Entertainment Tonight or The Insider or some such.
And a lot of other small scenes were cut out, probably because they would have pushed the movie into R territory. I remember one scene, after Neville gets back and has to deal with Sam after being infected, where Neville gets really drunk, and then pulls the knife blade out of his leg with a pair of pliers. He then heats it until it's red hot over a bunsen burner, and sticks it back into his wound in order to cauterize it. It was a real great little scene that I really wanted to see.[/blackout]