Well, taxes also don't automatically get removed from your bank account either...
It would be the same if Bitcoin became universally used. Governments would just accept payment in Bitcoin, but you would be responsible for making those payments and reporting your income etc.
Also, isn't it nice that they have this big ledger (blockchain) to see what kind of income you have received.
There would still be some people who would see it as an easy way to evade tax system and probably be able to cover up their tracks and get away with it. Governments still get value added tax from goods purchased anyway and that is something.
Moreover, I believe there may be some system in place eventually to help track some of those things, but this is based on assumption as I cannot think of one. Who has the tax paying helped anyway, except for some set of thieves using our taxes to enrich them-selves? In summary, no one cares about the government anymore?