I think that I will mirror what others have said to a degree. You do not have the nuts but you do have a strong hand. In these cases I feel there are two strong reasons for betting straight out and not checking the hand.
1. You have top two pair and there is a very good chance you have the best hand at this time. You should therefore put money in the pot for value. If others will call with second best and drawing hands like KJ, AK, JT, AJ, etc then you should get value from them. Your opponent can have a reasonable range of calling hands since he knows he will act last.
2. It is such a mistake to give a free card to a drawing hand here. There are two broadway cards on the flop and if there are two suits (or 3 to a suit flop) then you will have a good chance of running into either a straight draw or flush draw and maybe both. You cannot give a free card here. Even a small bet is so much better than a free card.
#2 above may be different if the board were K93 rainbow and I held say 99. Now my holding is stronger and the board is not coordinated at all. I can afford to give a free card here or at least give a cheap card. I probably bet 50% of the pot here. In this case I am only losing to one hand (KK) and the best anyone can draw to is maybe a gutshot. I also will fill up or make quads a reasonable amount of time.
With this in mind for your example holding QK on a QK6 board then I bet here nearly all the time. As for bet size I would say at a minimum I bet 50% of the pot but probably not more than 75% of the pot. I am not a fan of check raising due to the risk that I give the turn away free and with little to no information being gained. What would you do if you gave the turn card free and it was a 3rd to a suit card that was an ace, jack, or ten? Yikes those are terrible cards for your hand.