I understand what you are pointing out, but you are quite wrong to claim that per capita taxation was the intention of apportionment. It's a wacko notion, but there are many such wacko arguments put forward on this forum, it's part of the fun of it.
To take your argument one step further, taxes paid could be converted into shares with more shares going to those who paid the most taxes and zero shares to those who pay no taxes. Each voter would then get the number of votes corresponding to his or her number of shares. It would do away with the whole notion of "one man, one vote", but what the hey!