Sailors have known of rogue waves for a long time. They happen a lot more frequently than every thousand years.
In general, waves are caused by the friction of the wind on the surface of a body of water. The longer and stronger the wind blows in one direction, the larger the waves can become. Because of the hydro-physics involved, the depth of the water is directly related to the size of the wave.
But waves are not uniform in their period (frequency) or their amplitude (height). If waves are traveling at different speeds and heights, a random confluence of two or more waves can result in their combining forces thus creating the rogue wave. Interestingly, those waves will still maintain their "individuality" and the rogue wave will usually separate back into its constituent waves.
Having sailed in the North Atlantic Ocean and seen its forces, I can believe that these huge waves occur more than once every millennia. For example, the infamous 1991 Halloween Gale/Storm, also know as The Perfect Storm, saw giant waves and the proposition is that a monstrous rogue wave caused the capsize of the Andrea Gail. When added to the examples in the linked article, these behemoths occur more often.
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