First, you are saying the if someone steals $1000, then the punishment should be to pay $1000. In other words, there is no punishment -- the thief only has to return the money.
Second, suppose someone steals $100 every day, knowing that he will probably get caught once a week and have to give back $100. That's a great deal for the thief -- he nets $600 a week! In this case, the only way to prevent the theft is to make it not worthwhile for the thief to steal at all. That is, make the punishment more than $700 for stealing $100.
Finally, your argument that punishment should be based on loss of potential has a problem. Suppose you steal a bicycle that costs $1000. Your argument is that since you would only pay $20 for the bicycle, your punishment should be based on $20, not $1000. Or, you could even argue that since you don't have any money at all, you would have never paid for it, so the potential loss is $0.
First, "proportional" is not the same as "equal". Trebled liability for deliberate harm has a long tradition in common law, and is generally considered to be within the bounds of proportional punishment.
Second, punishment is only one part of the equation. It comes
on top of the requirement to "make the victim whole", meaning that (in your first example) the thief must return the $100
in addition to paying the $100-$300 of proportional punishment.
Finally, from the last example, the thief didn't steal $20 or $1000. The store was deprived of a bicycle, their property, and consequently was unable to sell it. If the reasonably expected sale price was $1000, then that is how much damage was done to the store; it makes no difference whether the thief would have been willing to pay that amount. The claim, however, rests on the loss of the use of the bicycle, not the loss of a potential future sale. If the thief had simply
copied the bicycle, or acquired a similar product from a competitor, the "potential sale" is still lost, but the store would have no claim.