I'll tell you what will happen.
Currently bitcoin (in most places) is taxed like a commodity, you pay capital gains.
This form of tax is too administratively complicated for a currency- imagine having to make a record of every single purchase you made, and the FX rate at that time. Furthermore, the 'reference' currency (local fiat) won't be around for ever so you wouldn't even have anything to compare bitcoin's value to. How do you work out the capital gains of a bitcoin if there are no fiat currencies!?
So in the long term it won't be taxed directly (via capital gains) but of course there will always be sales tax, income tax, on bitcoins/paid received, just like there is now for fiat.
I agree! Indirect taxing is the future it seems to tend to.
It's not a stupid way to tax your citizens though: the only one paying the taxes are the one spending money so it's directly proportional to your amount of money!
Moreover, it allows government to classify kind taxes. You can decide to tax more the Iphone and less or not at all the groceries for example ^^