It never was really zero, even with only satoshi and gavin on the network it still was worth a minute amount to them because they kept spending electricity to generate them.
Millibits are fractions, and that is moronic, and only a hardline Bitcoiner can think otherwise, ask anybody else if they want to use milli, micro, nano or femto-somthings. But that's beside the point, the point is if you create a unit of measure you would want it as close to real world applications as possible. And as it turns out that Bitcoin was made to work for a small community of enthusiasts for self-reliance. What actually happened a broad public came to use it and the way they have adopted it it makes them even more dependent.
This is also in tune with the software architecture of the main client.
My signature is just my way of making fun of the ridiculous notion that bitcoin would ever be a threat to the status quo.
I think those who ran the client in 2009 did not even consider the cost of running it. If anything the cost was measured in a slightly slower computer, a warmer room, or more likely a louder fan. So it was running at a loss. I don't think you can really say it was never zero or less than zero. Nobody would have bought those coins. Many transactions were sent around the network just for fun to test the client. Back then there was a send to IP feature (now removed due to MITM attacks) and it was cool to just experiment with it.
Have you read Konrad Graf's work "On the origins of Bitcoin"?
We don't know the final price range so it is not going to be easy to determine what unit of measure to use right now. But many countries operated in the million denomination range for small purchases (e.g. Turkey ~10 years back, then they dropped a bunch of zeros). Doesn't that also seem silly? But people can use it and adjust. Why be so concerned about the introduction of a decimal point? "Ask anybody else if they want to use hundreds, thousands, millions, billions, trillions." What's the difference between that and milli, micro, nano... sure the problem is that they have not been used before in money denominations so it seems strange to people. But people will just call them millies or whatever and not even think about the fact that the name is a derivative specifying a fraction of a bitcoin. We are deflationary so we are moving in the opposite direction.
Even with gold an ounce is a lot. So people sometimes talk about grams to specify tiny amounts. It is strange because they are using two different measurement systems when jumping from one to the other. But it is useful so they do it.