From reading over the decision, the judge emphasizes that a security is an investment contract. The institutional investors and Ripple formed a contract, in which the investors were promised that Ripple would do various things in exchange for the investment.

On the secondary markets, people were just speculating on the token price going up or down. They weren't getting any promises from Ripple, or even necessarily giving money to Ripple, so there was no contract. If there's no contract, there's no security. Just speculating on the price of something doesn't turn that thing into a security.