The reason Jonathan faced Speedwagon in the first place, and even got a deep injury on his arm and bone? He went to the forbidden alleys of London. The reason he did this? To prove Dio was poisoning his father and save him. It is his love for his father what pushed Jonathan to go this far and endure all the pain.
After Jonathan's father gave his life to stop Dio from killing him, the police lament that the kindness he showed to those around him was gone forever. Speedwagon, however, disagreed strongly.
Speedwagon: You're wrong! All that was good in that man, he passed along to Jonathan! Every bit of it! You can be sure JoJo's gonna live an upright life using what his father gave him! Rich folks are rubbish...watching them flounce about, I wanna throw the whole lot of them into the Thames...but not the Joestars...they're heroic, and merciful, and just...the whole damn lot are giants among men!"
Speedwagon's speech really speaks volumes of the Joestars that come after Jonathan. Sure, most of them don't act like gentlemen, one has temperament issues regarding their hair, another has plans to join and reform the Italian Mafia, and one doesn't even act like a proper lady, but at their core, they have inherited Jonathan's compassion, humility, and strive for justice, in one way or another.
In their youth, Dio all but destroyed Jonathan's relationship with Erina when he stole her Sacred First Kiss. As adults, however, Jonathan reunites with Erina as she nursed him back to health after his first battle with a newly vampiric Dio, and the two rekindle their relationship, ultimately ending in marriage by the arc's end.
When the life-force of Jonathan's Sunlight Yellow Overdrive restored Bruford's humanity, the once-more Proud Warrior acknowledged Jonathan as "a friend from another time", passing his sword "Luck" onto him, and crumbled peacefully into ash without hate for the world.
In a rather sad and twisted way, the ending to Phantom Blood showed that even Dio is capable of love, even if it's distorted by the childhood abuse he's suffered through.
Wang-Chan!! I will not tolerate you humiliating Jojo!! For being able to reduce me to this state, I respect him more than anyone in this world. Now show him the respect he deserves, and give him a quick, painless, and dignified death. Have I made myself clear?!!
The look of shock and then sadness on his face when he realizes that Jonathan has died says that Dio was far more human than he would admit.
Although it was momentary, the Time Skip after their childhood was very sweet to see, that Jonathan grew up strong and smart, getting past his past grief, and in the same time, it seemed that Dio made amends and they become steadfast brothers as they win their final rugby match for their colleges together. Of course, it all goes to hell when Dio reveals in monologue that he's still the same slimebag he was in child (and Jonathan is still rightfully suspicious of him despite feeling bad about it) but still, the rugby match was an effective heartwarming scene to lure the audience into a momentary sense of security that the two bitter brothers seemingly making amends and walking to their own bright future.
Jonathan's Heroic Sacrifice is just as heartwarming as it is tragic. If not for that, Erina and Lisa Lisa would have died, The other JoJos would have never been born, and the entire series would have ended then and there. Dio may have a lasting impact on the series, but so does Jonathan.
Danny and Jonathan's relationship and backstory is full of this. They started off on the wrong foot, with Danny biting Jonathan and the latter being scared of him and teasing him as a result. However, when young Jonathan was about to drown, Danny rescued him. Since then they became great friends, and Jonathan has sometimes felt like he was his only pal. Obviously this is just meant to make it hit even harder when Dio burns Danny, but even then, this and Jonathan's reaction comes to show how much Danny meant to him.