Maybe the content of the Howler was unexpected and shocking for Mrs. Weasley, causing her to break down in tears. It might also have touched on a sensitive topic or personal issue.
It could be that Hermione's Howler contained something really hurtful or embarrassing that made Mrs. Weasley emotional and shed tears.
It's possible that the content of the Howler conflicted with Mrs. Weasley's expectations or values for Hermione, causing her distress and resulting in tears. Another reason could be that it brought up past issues or tensions that were unresolved and finally boiled over.
Hermione could be very hurt. She respects Mrs Weasley a great deal, and to receive such an angry message from her would be a big blow. So she might cry and isolate herself for a while to think about what she did wrong and how to make it right.
Maybe Hermione made a decision regarding Ron that Mrs Weasley didn't approve of. For example, if she rejected Ron's marriage proposal in a rather harsh way, Mrs Weasley, who was very fond of Hermione as a potential daughter - in - law, could be extremely disappointed and angry.
In a fanfiction, the howler could have had a physical form beyond just a shrieking letter. It could be that when it arrived at Hogwarts, it took on the form of Molly herself for a brief moment. She could have given Ron a stern look and a lecture in person (sort of) before disappearing again. This would add a whole new level of drama and magic to the concept of the howler in the Harry Potter universe.
One possible fanfiction idea could be that Molly's howler in Harry Potter was actually a warning not just to Ron, but also a veiled threat to a dark wizard who was secretly infiltrating Hogwarts. Maybe this dark wizard had a plan to use Ron as a pawn, and Molly sensed it through her motherly instincts and magical awareness. So the howler was her way of sending a message to both Ron and the hidden enemy.
There's also a chance that she'll be hurt. Mrs. Weasley has a big heart and Harry ignoring her could really wound her. She might then become more withdrawn herself, focusing on taking care of her own family and leaving Harry to his own devices, while still secretly hoping he'll come around.
One scenario could be that Hermione is being bullied by some pure - blood supremacists at Hogwarts for being a Muggle - born. Mrs Weasley, who has always been inclusive, finds Hermione crying in the library. She sits down with her, hugs her tightly, and tells her that her blood status doesn't define her worth. Mrs Weasley might also offer to teach Hermione some of the Weasley family's special spells to make her feel more confident.
I'm not sure of a specific 'Mrs Weasley comforts Hermione' fanfiction off - hand. However, you could try looking on Archive of Our Own (AO3). There are often many well - written fanfics in the Harry Potter fandom. Maybe in one fic, Hermione has a fight with Ron or Harry and Mrs Weasley, being the kind - hearted woman she is, takes Hermione under her wing and offers her some words of wisdom and a warm cup of tea to soothe her.
A great Hermione stands up to Mrs Weasley fanfiction would incorporate the magical world's backdrop well. It could be set during a big family gathering at the Burrow. Hermione might stand up because of a difference in opinion about how to handle a magical creature situation. The author should also explore the emotions of both characters - Hermione's determination and Mrs Weasley's shock or disappointment, and how they resolve those feelings.
There are various types. Some might focus on the emotional impact of the Howler on their relationship. Others could explore the mystery or adventure that ensues from it.