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PDF said:

I though you were accusing me of massive spoilers.

I missed that the first time around but just rewatched the ending through illegal means - i feel a bit dirty

That being true, the humans would have gone into the redwoods right away to track down those apes to kill them.

At least it dones set up for the next movie in the series.  Battle for planet of the apes

While they surely woudl have went hunting, the redwoods would have provided a lot of room for these highly intelligent apes to stand their ground, hide, evade, etc. Then within a month as the massive virus would have been infecting the entire world... they would not have been a concern anymore. Additionally, as the virus spread to areas with more apes... they would be contracting it too and becoming intelligent as well as beginning their own reprisals against the falling human race.

Its this combination of the dual affect of the virus and the timing of it all that causes the eventual outcome. It really does fit together nicely.