What if someone who is Atheist is capable of good governance?

That's the unfortunate thing - most polls I've seen still have atheism as a top negative for a candidate (here's an example). In North America, especially in rural North America, if you're an atheist you are lacking in moral character because morals come from God. So you could be the best candidate for the job by a fair margin, but be considered lacking in integrity due to your atheism and so don't get the votes you need. Not to mention that despite being illegal, churches will have their own opinions for their congregations on who should be voted for - and you can imagine how they would summarize an atheist candidate. I know it's better in manner parts of Europe, but in N.A. atheism is still something that's put under a public lens as being a bad personal character trait - bad ethos. In both Canada and the US, you have to be a Christian (on paper at least) if you have a hope of running the country.

A candidate considering office has to be aware of the cultural pulse of the people he hopes to represent. They have to feel like they can trust him, and if you deviate from the core values of these people you in any way, you make it harder to win that trust. Using a different (but equally sad) example from atheism - you could have a naturally great governing ability, be a tireless volunteer and committed public servant, but if you are gay and especially if you live someplace like Indiana... Your political worth has already been judged based on your perceived personal character.