I'm Iso rank 11 now, but I definitely remember being in the negatives at the start of the Dominion League season. It's probably because I play mostly in real life and on Androminion. (and on Isotropic... RIP) All the other players were like 20 ranks up on me, and it felt like I belonged in E or even F division.
Playing on Goko, I have definitely noticed the catch-22 in raising up a low rating: you can't play people who are 4k+ because you aren't there yet, so you can never get to 4k+. I managed to break the barrier by playing in Dominion League, but for a while I felt really bad cause my rating would fluctuate wildly and I'd think that I was sapping my opponent's rating. That's probably why everyone only plays 4k+; they don't want to randomly lose to a 2k rated player and drop suddenly.
Also, some players are just good at some kinds of boards and bad at others; I love engines and combos, but I still don't really understand BM or alt-VP too well. So maybe when you play a low rated player, you just happened to play them in their area of expertise, and they were competent. But put Rats on the board, and watch them flounder around helplessly (in Androminion, Ambassador/Masquerade+Rats is an insta-win combo...)