I think it's too early to panic. Having practiced before the USPTO for over 20 years, I've seen many times how the small inventor lobby works its magic to protect the small filers. In fact, I was disappointed that the article didn't even mention the two-tier fee system, providing smaller fees for small businesses, that's been in place for many years now.
The PTO needs lots of fixes, but I agree that somethings need to change with the fee structure. Large companies can game the system by flooding the system with new applications, re-filing to wear down examiners, and taking frivolous appeals. Wise changes to the fee structures, which take into account these sorts of tactics, as well as increasing maintenance fees to discourage "wait and see" litigation, will be helpful to the small guy. Hopefully the PTO will show some wisdom.