It's my understanding that the SpaceX team draws at least some inspiration from the F-1 design. There's a mention of the F-1 under the Merlin 1D section of this Wikipedia article:
http://en.wikipedia.org/wiki/Merlin_(rocket_engine_family)#M...
The next time Elon Musk does an AMA (or something similar), I'd love for someone to ask him about the F-1. It would surprise me if every rocket engine designed since the F-1 simply ignored all previous designs. We may not have a complete, detailed understanding of the design, but the article comes across a bit on the "breathless amazement" side of things.
A lot of the comments here follow a common pattern where a layperson looks at a system and makes seemingly rational comments, but in reality they have an inadequate understanding to even form a relevant opinion.
I certainly don't have enough understanding of rocket engine design to hold an opinion. Even after reading that piece, I must consider the source and the tone of the article. Also keep in mind that programs within NASA are, in essence, in competition with companies like SpaceX.
SpaceX has plans for bigger rockets and engines, but those are rumored to involve different fuels, perhaps for reusability. (Kerosene, the fuel for the F-1, and the Falcon 9's Merlin engines, gunks up the engine's innards a lot more than liquid methane, which is the rumored fuel for their next generation engines. If de-gunking would require a rebuild after a few flights, it's something you might prefer to avoid. The technical name for "gunking up" is "coking", if you'd like to read more on it...)