There is perhaps nothing that Star Trek content creators fear more than the collective power of Trekkie nerd rage when the universe's canon is altered. Cryptic Studios is well aware of this and wants to clarify where Star Trek Online falls in the IP's timeline, and they frame this in reference to the latest (and eleventh) film and the deviation from canon it introduces with an altered timeline.
Plainly stated, Star Trek Online adheres to the standard timeline. STO will be set in the same reality as the first ten films and the various TV series, from First Contact right through Voyager and beyond. Cryptic Studios has put together a graphical timeline of the entirety of the Star Trek legacy, showing exactly when the game picks after the shows and films leave off, with the events of Star Trek Online taking place in 2409. Have a look at Cryptic's Star Trek Universe Timelines for more.