Yesterday I was on a passenger plane flying at 35000 feet from Denver to JFK on a fairly clear day. Just west of Sioux City, we made a relatively sharp, but short, right turn for whatever reason (may be unrelated). I happened to be looking out my window and caught what appeared to be a military fighter jet (presumably from the Air Force base there) flying in the opposite direction. It blew past my field of vision in a fraction of a second, slightly below us and off to the right, close and fast enough to startle me. It left a beautiful set of trails but, while my distance judgments aren't very good from a plane, appeared to be no more than ~1000 feet away from us (based on its size, I imagined it to be about 4-5 NYC city blocks away, that's my only reference). The passing aircraft's trails were dead straight at least as far back as they extended before dissipating. I didn't get a chance to ask the pilot about it after the flight.
My only knowledge of separation laws is from wikipedia, which seems to state a 2000 foot limit above 29000 feet. I absolutely might be misjudging distance, but this aircraft seemed to be well under a half a mile away. So my question is: Are there a different set of separation laws for military aircraft, or perhaps are existing laws just not as strictly followed / enforced by the military? Would the pilot of one of the aircraft expect some sort of reprimand later? Was this a normal occurrence or was it a close call?