Yeah, it's tricky. Over time, I've become better at distinguishing obvious trolling from sincere questions, though I'll never be 100% accurate at spotting the difference.
A big factor is just "Are they responding to what I actually wrote?" because most of the trolls will see "trans" in my article headline and leave a brief comment about "save the children!" when their expressed "concern" isn't related to the topic of my essay—or, alternatively, was something I already addressed in my essay so they shouldn't be raising it from scratch.
Also, a troll will typically answer their own question and then say something like "Of course, it's best to be open-minded! Like me! Not like you, you closed-minded trans person!" which means they don't want more info from me (so why are they commenting? why would I respond?). Whereas a sincere person will actually spend a few minutes reading what I wrote and carefully phrase some relevant critique.
I also feel like the moral panic, and the megalogue about it, has moved into a stage in which "I identify as a concerned parent" is decreasingly a plausible excuse for leaving "Just asking questions!" on trans people's articles. Just about everyone knows where they stand by now, approximately 7-ish years into a mass moral panic. If they truly are a concerned parent, they can find appropriate ways to address their concerns (like, go find a good-quality book or documentary?) that don't involve bothering random trans people on the internet and trying to make us cough up some oversimplified or rude statement so they can feel justified in hating us.
I do try to be non-rude to people who are being real. I usually avoid being rude to trolls, too; I just block them.
People with real questions/uncertainties should (please, I hope) remember to embrace some responsibility for considering how overwhelming it is for marginalized people to deal with "just asking questions!" all the time from anonymous/pseudonymous handles. I can easily spend an hour (or five) contemplating a good response to their question...but did they likewise spend an hour thinking about how to phrase their question? 🤔 Or did they spend a mere two minutes, and is their lack of attention what makes their question so confounding to me? Where I guessed wrong about them being a troll, it might have been due to them not having put the time in on their end to initiate whatever meaningful conversation they might have wished to have. I say this to be gentle with myself and to be realistic about how "fair" I can be with commenters who don't make much of an effort to distinguish themselves from trolls. What indeed would it mean for me to be fair with them? If they gave me 2 min (including not-reading my article and typing a self-contradictory comment), I give them 2 min back, tops? Sounds fair :)