I noticed since 12.11.11(didnt get game on 11.11.11),

dragons have attacked everywhere in every settlements and cities, except for markarth. I never ever saw ONE dragon attacking markarth city, though karthwarsten got hit. I tried every ways to make a dragon spawn legitly, like fast travelling to markarth etc. It works for other cities but not markarth.

Is it meant to be like this? If so, how come some people reported dragons attacking markarth?

They probably just gave up because its such a pain in the ass killing anything there as a dragon, lol.

Ask the jarl if he's worried about a dragon attack. He'll tell you why it's not a problem. I imagine the dragons know this two and so they don't bother

Markarth can get hit, but the chances are quite low (same for Whiterun and Riften, for me at least).