The shift happened quickly and it is worth being precise about why. In its economic analysis of a 2022 proposal, the SEC recorded that "PFOF brokers led discount brokers into zero-commission trading in 2019", and noted the dependency running the other way as well: if payment for order flow were to stop, some discount brokers might resume charging commissions. That is the clearest available statement of the relationship. Commission-free pricing is not a discovery that trades are cheap to execute. It is the substitution of one payer for another.
Where the money comes from is not secret, and published disclosures list it. Payment for order flow is one source, and our page on it covers the mechanism and the disclosure rules. Interest on uninvested cash is often larger: a broker that sweeps idle balances into its own bank or a partner bank earns the spread between what it pays the customer and what the money earns, which is why the default sweep rate on a cash balance is worth checking. Margin lending charges interest to customers who borrow. Securities lending earns fees from lending customer shares to short sellers. Fund revenue sharing pays the platform for distributing particular funds. Premium subscriptions, options contract fees and fees on foreign or over-the-counter securities fill in the rest.
Two charges are not the broker's revenue at all and survive on sales regardless of the commission model. Section 31 of the Securities Exchange Act, at 15 U.S.C. 78ee, requires each national securities exchange and each national securities association to pay the SEC a fee calculated on "the aggregate dollar amount of sales of securities", at a statutory rate of $15 per $1,000,000 that the Commission adjusts under subsection (j) to match its appropriation. Brokers pass that through to the selling customer, which is why a sale confirmation carries a few cents of fee and a purchase confirmation does not. FINRA levies a separate trading activity fee on its members on the same one-sided basis. Both are small, both change periodically, and neither is a commission.
The cost that dwarfs both is the spread. Buying at the offer and selling at the bid means giving up the difference each time, and on a thinly traded security that difference can exceed anything a commission ever was. Our page on the bid-ask spread covers how it works. The point specific to this page is that removing the commission removed the one cost that was itemized, leaving the larger one invisible.
There is a behavioral consequence too, and it cuts both ways. A per-trade charge is friction, and friction discourages trading. Removing it lowers a real and regressive barrier for someone investing $200 at a time, and it also removes the pause that a $9.95 charge used to impose on an impulse. Both effects are genuine, and which one dominates for a given person is not something a pricing model decides.