I think you're just not considering the whole pot. If you assume none of the starting $1.00 pot is either of yours, you have to count it for both of you. So like your example, the pot is $1.00, you raise $1.00 and he calls with a 33% chance of hitting the flush or straight. Say this is done 10 times.

He will win the $3 pot 3.3 times or $9.90.
You will win the $3 pot 6.7 times or $20.10.

So, if you assume the original $1.00 in the pot is neither of yours, it cost him $10 for these 10 $1.00 bets and he loses $.10.

Now lets say the two of you were the .25/.50 blinds, everyone folds, and the small blind calls, and you in the big blind checks. Now you each end up with the 10 bets costing you each $15.00. Now he loses $5.10 and you win $5.10 overall. I think this is the way to look at it since it sounds like you knew you had TPTK and that he might be on a draw.

If the odds were 50/50 you each put in $15 to win the $30 worth of pots.

I hope this makes sense and that I explained it right. I think it's difficult to get the exact numbers when calculating pots odds in this manner because you don't normally count how much is in the pot because I think it's assumed that you both put in an equal share up until this point, also the same way if there was a third person that might call your raise of $1.00.