The story tends to focus alot more on Gyro, his actions, hardships and past quite a bit more than Johnny. He was also introduced first, during the point when Steel Ball Run wasn't officially announced as part of the JoJoverse yet, so many believed he was the main character.
Simply put, if someone who wasn't familiar with the whole "JoJo" thing read it, they'd assume Gyro was the main character. I would say the two share the main protagonist spot, as it says on Gyro's page.
To follow up on Kaiser's point, Johnny wasn't even a official "JoJo" until volume 5 of Steel Ball Run. Johnny was nowhere near as badass in the beginning as he was after the Seinen switch, well... as compared to Gyro at least.
So, it is as if he was initially "THE" main character when SBR was its own series, but was downgraded to main ally after it joined with JJBA ? or does SBR continue to focus on him after it became Part 7 ?
It continues on Gyro as the main character even after it was officially Part VII. Just Johnny is not a side ally anymore but as a JoJo. Like instead of The Hero (Gyro) & Sidekick (Johnny) story, they are partners & equals.
Bassically the first part of Steel Ball Run up to the final duel with Valentine and D4C Lovetrain, is really the story of Gyro. Steel Ball Run mainly follows him and Johnny, and while Johnny is the main Joestar of the part, his role is supposed supposed to be that of Gyro's selfish immoral equal. Bassically think of SBR as Star Wars Revenge of the Sith. Johnny is the character of Anakin and Gyro is Obi Wan Kenobi. The story is divided among the two, follow both as protagonists.
Araki wasn't even sure that SBR, in the first chapter or so, was going to be a part of JoJo, and Gyro was initally introduced as the main protgonist.. Johnny eventually takes up Gyro's mantle of main protagonist, and evolves his stand to a very powerful level, then has it out with both Valentine and Diego, as well as trying to improve himself and become a better person near the end of the part