If you think this movie had a happy ending, you're an idiot
I'll buy it if you didn't think the ending was dark enough, but this movie in no way shape or form has a happy ending. I get if the ending is transparently dark, you think it makes you deep for appreciating it, but to call the ending happy actually makes you pretty dang shallow.
Seriously, look at the ending. The entire world is afflicted with a singular infection. When they fix it, does it turn into a happy ID4 ending?
No, humanity pretty much picks up right where it left off. It's actually more depressing than the everyone gets infected ending. It's bittersweet at best. The thing is, yes, Nicole Kidman cures her son and they save themselves- but she's left with the realization that it's at the cost of people's tendency to destroy themselves on their own.
Why is the downer of that ending so hard for people to grasp? It was pretty much saying we don't need to worry about a greater being, we're destroying the world without any help.