Absolutely every single person in a position of power, whether it be Joffrey, Ned, Tywin, Robb, Dany, or whoever else, is coming from a place of entitlement and ego. That is the nature of kings, queens, and rulers. They are fundamentally incapable of fully appreciating and empathising from the perspective of a commoner because of their entitled "right" to power and royalty. Even "good guys" like Ned and Robb still have moments where they demand people kiss their arse, bend the right leg, and generally make it known that they, in all their righteousness, call the shots. Tyrion could very well be the only person who bridges the gap, or at least comes closest to.
Dany watching her brother get smelted is hardly Joffrey level sociopath. He was a gigantic cunt, a threat to her, her well being, her power, her relationship, and the Targaryen empire as a whole. He was a fucking idiot blinded by entitlement at least no different to her own, almost always far worse, coming from the position of someone who simply hadn't endured quite as much as she had, at least so recently.
Ultimately though Dany is supposed to have flaws, I feel, just like everyone else. Ned was flawed too, despite being the clear protagonist/hero of the first season. He was foolishly bound to a shallow perception of laws and rules and order and was willing to cut off a head without a trial, without discussion, because thems the rules that daddy's daddy's dad (and so on) upheld. He was too simple and honourable to play the politics game at Kings Landing. Robb let a similarly childish view of honour and justice overrule sensibility in war time when he knocked off Karstark's head and then tried to undo his insult to the Walders as if it were no big deal, despite his wiser, more experienced mother telling him on both occasions not to fucking do it.
Dany's fault, so far, is that she really is an exceptionally inexperienced and fairly terrible Queen. She's been city hopping freeing slaves and winning people over with honour and nobility and empathy yet has done sweet shit all to actually lead a civilization. She hasn't had to rule, enact laws, deal with fairness and rights, because everything so far in her journey has been fairly black and white. I feel this is why her story arc is where it's at: she now is faced with the realities of life, of being a Queen, and evidently is not very good at it. She's exposing her empathetic flaws, hence why the likes of Jorah are advising her otherwise.