One of the biggest problems that I have with the "free" argument, which you've mentioned in your article, is the whole idea of marginal costs of zero, or virtually zero. Generally speaking (and I can't think of a good counter-example), the only way that you get to such low costs is through significant capital investment and mass production so that, over time, fixed costs are distributed over a huge volume of product.
Anything that's mass produced, or mass distributed, still requires a rather large up front investment. That takes deep pockets, which many smaller companies don't have. You've indicated this above in your comments about Gmail overpowering Yahoo Mail (although Hotmail is still around...?)