It protects the top of book only, and it protects the quote, not the investor's whole order. Exceptions are broad: intermarket-sweep-orders, benchmark and auction trades, self-help against a malfunctioning venue, and flickering quotes all qualify.
The rule is why brokers must either route out or sweep before printing away, and why sophisticated senders use ISOs to take multiple price levels at once without waiting for a routing round trip.
Example: best protected offer is 12.30 for 500 shares; a dark venue has 20,000 available at 12.31. A plain fill of 20,000 at 12.31 is a trade-through. Marking the order as an ISO while simultaneously sending 500 shares to take the 12.30 makes the 12.31 fill compliant.
Related: trade-through, protected-quote, intermarket-sweep-order, reg-nms