It's important to differentiate between beliefs and reasoning. The problem isn't that people mistakenly assume that they are the same, but rather that people can assume that having "good" or "right" beliefs as ends in themselves, regardless of the reasoning process that produce them. I won't dismiss the value of having good rather than harmful beliefs, but relying on unsound reasoning processes doesn't leave much room for improvement and learning.
As an example of how this problem can appear, consider how atheists tend to view liberal, progressive Christians in a more sympathetic light than they typically views fundamentalists. After all, liberal believers generally support civil rights for gays, church/state separation, etc. There is a lot of opportunity here for making common cause on many political and social issues.
The fact that liberal believers hold sensible political positions, though, doesn't mean that they practice sound reasoning. However much we might support and agree with their progressive political and moral positions, we shouldn't ignore the fact that if those positions were arrived it for the wrong reasons, we may be in for different problems down the road.
In Losing Faith in Faith: From Preacher to Atheist, Dan Barker writes:
There is a place in the Bible where God says, “I know thy works, that thou art neither cold nor hot: I would thou wert cold or hot. So then because thou art lukewarm, and neither cold nor hot, I will spue thee out of my mouth.” (Revelation 3:15-16) To the fundamentalist, liberal Christians are worse than atheists.
I remembered having despised liberals who have “a form of godliness, but denying the power thereof,” and who offer more of a temptation away from devout faith than any atheist could pose. At least with atheists, you know where they stand. Attempting to learn what a liberal Christian believes is like trying to nail jello to a tree.
One can also phrase this going the other direction: at least with fundamentalists and conservative evangelicals, you know where they stand and what they believe. Their political positions might often be odious, but those positions generally follow logically from specific theological doctrines. What this means is that there is at least a chance for logical arguments to have an impact — the more they rely on logic to defend their position, the more vulnerable their position is to logical critique.
When it comes to more liberal believers, however, the picking and choosing they do with religious scriptures is even more extreme than what you find with fundamentalists (everyone does it, but some do it more than others). Ultimately their "standards" for their interpretations come back to whatever moral and social beliefs they have absorbed from their culture, but they don't recognize or admit this and instead attribute those positions to the authority of their scriptures.
So just how firm are those conclusions in the end? I'd argue that they are less firm than with others who derive their values from culture because others at least recognize where their values are coming from — they aren't pretending that their values have some sort of transcendent, supernatural source. This is why having the “right” conclusions isn’t necessarily as important as using the right methodology. A person who uses irrational thinking and methodology to arrive at the “right” conclusion can’t be trusted to hold that conclusion. The persistence of evidence, facts, and science just wouldn't matter.
What's more, it will be difficult for them to improve their positions in the future as we learn more. A person whose positions are based on science and evidence can change when the evidence shifts; a person who attributes their positions to a reading of the Bible which is unconsciously tuned to justify prevailing cultural winds can't be counted on to change when the evidence changes. They've already invested a lot in particular scriptural interpretation and will first have to admit error in that before they can adopt a new moral belief.
On the other hand, a person who uses clear reasoning and coherent thinking to arrive at the “wrong” conclusion can be more readily engaged in a substantive discussion over the issues. A person who has arrived at the wrong or at an immoral conclusion based on mistaken evidence or faulty reasoning may, if they are intellectually honest, be corrected by being shown accurate evidence or sound reasoning.
Thus while we do want to encourage people to adopt the right or moral beliefs, I think we need to invest even more effort into encouraging people to adopt the right methods for forming, evaluating, and defending beliefs. It's better that people have the right tools to deal with faulty beliefs than that they have good beliefs but lack the tools to improve and development them over time.