So, even in a perfect world where BTC is the only currency, don't you think there should be a way to let everyone pay their taxes? Then HOW, that's the tricky part! Directly - you pay depending on what you earn - this could be done by your employer OR indirectly -you pay when you consume - like VAT? Dunno... 
Why do taxes have to depend on what you earn? Why not just have a simple system where everybody owes the same amount of money every year, wouldn't that be more fair?
The how of paying taxes with bitcoins is really easy: the government sends each citizen a bitcoin payment address, they send the bitcoins owed to that address.