Facebook is whining, not because Apple will "harm the free internet", but because Facebook's ability to rack up billions in advertising revenue will be impacted.
"To make ends meet, many will have to start charging you subscription fees or adding more in-app purchases, making the internet much more expensive and reducing high-quality free content."
Translation: Because of this change, more businesses will discover that Facebook advertising isn't worth what they claim it is, so they'll charge consumers directly for their service. That means revenue will go into the businesses pockets, rather than business revenue going into Facebook's pocket.
The other benefit is that websites will have to offer services that are of sufficient value that consumers are willing to pay for them. As it stands now, there are too many sites with sub-standard content that survive because of pervasive advertising. You want my subscription dollars? Offer something of value, so I'll be motivated to pay for it!
To be clear: Facebook's complaint has nothing to do with a free internet or small business owners. It's 100% about Facebook's ad revenue being reduced because consumers don't want their privacy invaded for the sake of Facebook's profits.