I think you have to look at these fights separately. After all, Fedor was past his prime when he came to Strikeforce, but he was still good, so that's not the main reason.
1) He thumped Werdum, then got aggressive, and got caught by a fantastic BJJ blackbelt. It could happen to anyone, champions JDS and Cain included, who gets too aggressive against a submission artist of Werdum's caliber.
2) Bigfoot was the one of these three who I will say was definitely a bad matchup for Fedor. Fedor is basically a light heavyweight in frame who was going against a guy who was 70 pounds heavier on fight night. Bigfoot is skilled enough to where he could use that size. That being said, I firmly believe Fedor would have won that fight had he been allowed to come out for Round 3.
3) Fedor hit Hendo HARD. I think Hendo said it was the hardest he'd been hit. Fedor had him in trouble, then was the recipient of a combination of over-aggressiveness (again) and a very unfortunate stoppage.
I would ask this: if Fedor fought any of these guys again, would he be the underdog? I think he would be against Bigfoot, and that's it.
It was a bad run. Fedor was too aggressive, but let's not act like these were one-sided beatdowns. There were two fights (Werdum and Hendo) against elite fighters who Fedor had in serious trouble, and there was one against a physical freak (Bigfoot) who was a bad matchup, and whom Fedor probably would have beaten in Round 3.
The biggest mistake the casual fan makes is believing that the win/loss result is dispositive of the question of who is the more talented fighter. Especially at HW, any top 10 HW could beat any other top 10 HW on any given day. So records lie, and while they're about talent and skill, they're also about odds and chance and luck. (I mean, just a year ago people were saying JDS was the HW GOAT, and now they're saying Cain is the HW GOAT, and three years ago they were saying Brock could be the HW GOAT. That's the nature of heavyweight.)
Long answer: Fedor lost some competitive and entertaining fights against some very good / elite fighters, and that can happen, especially if you go in with a bad gameplan, are over-aggressive, or have a poor matchup.