It's because one guy, named Hicham El Guerrouj, retired. Breaking 3:29 is really hard, to the point that there have only been 20 races in which anybody broke 3:29, and El Guerrouj was in 15 of those 20 (winning all but one). He dragged most of those other sub3:29s behind him.
What was Bekele doing in 2006? He was dialed into the Golden League trying to win a share of half a million dollars, running 12:58 in Oslo (for second) on June 2, 12:51 in Paris on July 8, 12:51 in Rome six days later, 12:48 in Zurich on August 18 (with Isaac Songook breathing down his neck), then another 12:48 a week later in Brussels, then a 12:57 to win the next week in Berlin, then a sit and kick win over 5000m a week later at the WAF, then by the time he got to the World Cup, he had nothing to fight off Mottram in the 3000m.
You've got to keep in mind: only three men have ever broken 12:40. It's extremely difficult and in addition to being among the most talented distance runners to have ever walked the earth, you also need to be in excellent shape. You also need to have excellent pacemaking, which is tough to come by, because if you're good enough to pace a world record attempt in the 5000m or 10000m, you're good enough to be in the race and possibly challenge. That day Bekele ran 12:40 in Paris, he went through 3000m in 7:32. If he had been just a bit slower, he probably wouldn't have fallen off as he did.
Bekele's still injured (as of earlier this month) and I doubt we'll ever see him again in the kind of world record (track) form we saw him in from 2004-2006. This new kid, Almirew, may be the next big thing. But again, good luck finding the right pacemakers for a world record attempt. You can get a lot of guys to through 1600m in 4:02 on pretty even splits, but try finding (and paying) a guy who can lead the next four laps and hit 7:34.0 for 3000m.
No one races over 2000m so who cares.