As stated, the important thing to remember is being an antagonist does not make you the “bad guy.” Iron Will becomes the antagonist because he begins the conflict and encourages Fluttershy’s behavior with catch rhymes. Of course, he also later drives her from her self-imposed isolation, thereby creating a climax of conflict that she has to resolve. We were reminded that Iron Will at least had a role because of her quoting rhymes implied to originate from him.
However, you do bring up an important point that Fluttershy was arguably her own antagonist because of how poorly she treated everyone for the most mundane reasons; that one scene especially where she deeply insults Pinkie and Rarity does not add up at all with her implied training. That was all her focusing her aggression to a pin point. (Honestly, it sounded to me like when someone hates a person but does not bring it up unless he/she gets in a fight, but more on that in a bit.) Of course, when she hid away in her shack, her fear of becoming overaggressive was the main source of conflict.
Let me reiterate an old pet peeve: this was the only episode in the entire series I genuinely disliked (although the Discord episode started to come close merely because of its focus on Fluttershy). It gives the impression that all this time Fluttershy acted not out of kindness but out of social pathology and ultimately does not care for anyone else except maybe her animals. The worst aspect is this episode was intended as character development: if TMMDW had the impact this episode did, we might have lost half the fanbase by now. This episode damaged Fluttershy’s character permanently; her once important moments of sternness and assertiveness have been blunter and even inconsiderate past this point. Later she would threaten Twilight, stampede over Rainbow dash, and ignore Rainbow Dash BEING HIT by utensils to berate her friends for not giving Discord a chance. Note I haven’t even brought up how painfully cliche the entire premise is or how redundant it is given the far more meaningful and in-character moments of assertiveness and strength exhibited by Fluttershy in the past.
To summarize and return focus, calling Iron Will an antagonist may sound harsh, but that is at least his nominative role. That does not necessarily mean that he was the only conflicting force at work, however.