I had a discussion about the ending of War of the Worlds (WOTW) with my co-worker, an older guy to give me his perspective on both the book and the movie. Basically what he wanted to get across to me was that although it may seem like a cop-out, when you consider when the book was written and what the point of the movie was, it wasn't really a cop-out at all.
After talking to him, I did my own bit of research. The book was written in 1898. This means the story is over a century old. Also consider other Science Fiction movies, they follow a similar "cop-out" ending. I was immediately reminded of the movie "Signs", when aliens attacked and were ultimately defeated by coming into contact with water. That was pretty disappointing. Moreover, the concept of water being their weakness was kind of unbelievable -- why would they invade a planet that is 80% water. They should have died when they travelled through our atmosphere. Or Independance Day, where all it took was to fly into the big gun of each of the big saucers. Also the use of a computer "virus" to "infect" the entire collective.
The narrator for WOTW offers a hint of the eventual demise of the alien invasion -- the images of amoebae in the beginning. Amoebic dysentery, which is essentially food poisoning -- consuming contaminated food that causes severe diarrhea. Now putting the pieces together, the aliens ate the humans by sucking their blood -- so we were their "food", and since many of us carry various 'contaminations', it was the aliens who suffered this amoebix dysentery --- they suffered from food poisoning.
It's interesting actually that after the WOTW I joked with Kenric that the disease that beat the aliens may have been common cold. The fact is in the original book, it *was* the common cold that beat them.
Another key issue is that back in 1898, we are talking about a time before "modern medicine", in which even humanity was suffering from several kinds of diseases that we have found cures, vaccines for since those days. For example, Penicillin wasn't invented/discovered until 1928.
So considering all the of the factors (of the original story, when it was written, and Spielberg's responsibility to preserve the essence of the book) the ending wasn't so bad. We take for granted things that we now have that people in 1898 didn't.