While I agree that Daenerys is not as bad as Cersei, and an argument to that affect can certainly not be made, viewing Daenerys as a positive force (which she has purposely been portrayed as) is just being purposely blind to what exactly Daenerys quest actually entails. She kills her enemies through incredibly brutal means (crucifixions, and burning them alive) as Cersei does (Cersei, of course, is far more brutal) and has no compassion for those who stand against her. Her goal from the very beginning has been to conquer a continent and slaughter her enemies simply because she believes she's entitled to rule them, but still wants them to love her in spite of this. She's not a very good ruler (as we see in Slaver's Bay) and even knowing the war that's to come she still insists in squabbling over the Iron Throne and puts Jon's unwillingness to bow before her over protecting the seven kingdoms she wishes to rule. If she fails diplomacy she is unwilling to compromise and instead simply burns her enemies alive. She doesn't try to give those in Westeros a reason to follow her, or a reason to love her, she simply demands it of them. Those who follow her consist of a horde of Dothraki (who have no choice but to follow her as she murdered their leaders, an army of Unsullied who knew nothing other than fighting and had nowhere else to go (and are in a situation where leaving means defying the individual they just saw burn the city; as Jon points out to Missandei, they're not truly free, they're just serving a different master), and people joining her simply because they hate the current individuals in power more. Yes she listens to some of her advisors to not burn down King's Landing, and to give Jon the ability to mine dragon glass, but if others in Westerns won't bow before her, how merciful will she truly be to them?
Daenerys comes across as good because those she faces are monstrous and (have been previously) relatively nameless, she has nice ideas and doesn't naturally want to incite violence (she just does it anyway) or kill civilians, her victories are portrayed very heroically and in an uplifting manner in the show, she's staunchly against the idea of slavery (but is still totally okay with ruling over others simply because her name is Daenerys Targaryen), and came from absolutely horrible beginnings which she managed to turn into what she has now.
The meeting with Jon very starkly contrasts him with Daenerys, and it's not accidental. Both of them have given freedom to others (the Wildlings and slaves), both can argue they have a right to a kingdom (the north, and the seven kingdoms), both have encountered some seemingly monstrous and savage people, but their attitude is entirely different, and Jon is in many ways what Daenerys aspires to be, rather than who she actually is thus far. He doesn't rule because he's entitled to it, or because he wants to do it, he does it because those around him respect him as a ruler, and if others wish to walk they can walk (and still have somewhere to go) and won't be executed or burnt because of it. He doesn't try to destroy or give brutal deaths to any who have defied or opposed him (Wildlings), and doesn't simply kill them as soon as democracy has failed (Mance, the defectors in the Night's Watch prior to their killing him). He doesn't wear his titles as a point of pride to try and leave others in awe of him. He simply wants to protect the realm from a substantial evil (as far as we know thus far).
None of this is to say that Daenerys is inherently bad, or is an incredibly evil person, it's clearly much more complicated than that as the season has thus far revolved around the internal conflict of her wanting to be loved and inspired by the citizens of Westerns and accepting her role as a conquerer (and a dragon; something especially relevant in a season where people have gained strength in accepting and drawing from who they are), but it isn't tough to see why people can legitimately argue that Daenerys is not the shining beacon she has been portrayed as up to this point.
