If you're otherwise healthy and would have a 1/1,000,000 chance of having the disease before the test, and then you test positive with a test that is 99% accurate, you are ~100x more likely to have the disease than before - but that's still only 1/10,000 - not at all 99% likely, even though the test was "99% accurate"
That said, I think with this knowledge the test still confers helpful information. I might decide to spend $1000 on an additional diagnostic, even knowing that I'm still very likely to be negative. Depends on how wealthy I am, and how serious the disease is, and what the treatments for it are.