At higher stakes the players are better. It is natural for everybody to have smaller relative win rates.
At penny tables the rake is relatively much higher compared to the blinds then in the middle limit games. Below is the rakes schedule for NLHE at poker stars. I stripped out the short handed rakes, just because they added to much clutter, and am just going with the max rake. I have left in the percentage that the rake is taken at. If you divide the blinds (BB+SB)\cap, you come up with a nice benchmark for how much one is paying in rake relative to the blinds. Were there is a range of limits I just used the upper limit for the calculation.
Stakes % Rake Cap Blinds/Cap
$0.01/$0.02 3.50% $0.30 10
$0.02/$0.05 4.15% $1.00 14.28
$0.05/$0.10 to $0.08/$0.16 4.50% $1.50 6.25
$0.10/$0.25 4.50% $2.00 5.7
$0.25/$0.50 4.50% $2.50 3.3
$0.50/$1 to $3/$6 4.50% $2.80 0.31
$5/$10 to $10/$20 4.50% $3.00 0.1
$25/$50 4.50% $3.00 0.04
$50/$100 4.50% $5.00 0.033
$100/$200 and above 4.50% $5.00 0.016
AS you can see from the numbers you are paying in the $0.02/$0.05 game the rake max is 14.5 times the blinds. The last penny game on the list is $0.25/$0.50 the rake is 3.3 times the blinds. As you proceed up in limits you will see that the rake becomes significantly less of a drag on the proper size bankroll for a game. Your win rate is a formula of how will you play in relation to the other players and the cost of the game in relation to the blind size. The blind size determines how much you and all the players are going to bet, and buy in for.
in the old days of limit play it was easy to figure out how much expert play in say a 10/20 limit game would net. The expectation on expert play was two big blinds an hour. With rakes like in the penny games, your overhead for rake would possibly have you loosing as much as 100+ big blinds an hour to the rake, leaving you a net of lots negative big blinds an hour to play penny games. However in NLHE this equation is not so solid, expert players dispatch bad player at a much higher rate. Just saying the extremes of what you can win or lose relative to the blinds are much higher in NL poker. However, in penny poker were you are paying 3 to 14 times the big blind each sizeable pot you win, it is not likely even an expert player will beat the grind. The reason you are not doing so well in penny poker is that the rake is destroying your win at a much higher relative rate then it is in middle and higher limit games.