Hello! I’m so sorry this took ages for me to get round to.
(Generally, the trickier/more interesting the question, the longer it takes me to reply… so… yeah ♥ I LOVE literary questions, you can always hit me with them if you don’t mind a bit of a wait)
I think you’re definitely not wrong. Rin is the S1 character with the clearest arc: low-neutral-high-DEEP DARK LOW-finding his way back to the light, the character who grows and changes the most, and the character with a goal that drives the storyline of the season - ostensibly, beat Haru, in reality, overcome his own demons.
On that note, I’m now gonna play devil’s advocate for a bit ‘cos although Haru is not as clearly inscribed in the protagonist model as Rin, I think maybe that’s because everything about him is just more… subtle, perhaps.
Haru does have his own plot-driving goal, which dovetails with Rin’s ultimately: overcome the demons of his past. He, too, starts on a pretty low note, and along the way, he is saved as much as Rin is by his friendships. When he and Rin have the climactic showdown by that tree in S1E12, Rin’s the one being dramatic, but Haru, in his own way, is finding his resolution in that scene too. It is his apotheosis of self-realisation, his Moment of Truth.
In every aspect, though, he is a lot more lowkey than Rin is, which leads naturally to him leaving less of an impression as a protagonist.
I’m now going to take this devil’s advocacy exercise the next step up and suggest that “protagonist” as a term doesn’t necessarily always mean “main character”. I think they are often conflated into one, but the thing that makes a protagonist is that the plot and the central conflict/crisis of the story revolve around this person, and their direct actions are the ones pushing it forward. The main character, on the other hand, is more simply the character whom the story spends most time on, or whose POV we see the most.
It has been suggested that in To Kill A Mockingbird, the main character is Scout, but the protagonist is Atticus. In Suzumiya Haruhi, I would suggest it is possible to see the main character as Kyon, but the protagonist as Haruhi.
In Free! S1, I think it is also possible to break it down that way, and to see Rin as the protagonist and Haru as the main character. I feel like this is the truest representation of S1. By S2, Rin becomes more of a deuteragonist, a character whose role is to support the protagonist.
But if you’re not so keen on splitting hairs, then I would be inclined to think of Rin and Haru as joint protagonists of S1, just that Haru is less visible than Rin in that regard.