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While I don't actually think that the OP carries the implication Aaron suggests it does, I think the general point about the upshot of the fact that systems of values are embedded in worldviews is correct, and important.
In this context it's worth remembering too that many atheists & theists alike are converts, and their value judgements about whether other people are living well are intimately tied up with their view of their own intellectual and moral trajectory; whether *they* are living well.
To use a non-religious example: I once got into a heated discussion with a friend who was getting very frustrated because I, as a vegetarian, wouldn't just admit that I thought it was morally okay for them to eat meat.
But I used to eat meat, too, and I stopped, even though it was difficult and inconvenient. And if I didn't think there was something wrong with the way I was previously living, if I thought that one of these forms of life was just as good as another, I wouldn't have given it up!
So it can be hard to discuss these issues with someone else, or even to confront them honestly on your own, because if you're just indifferent about which of these worldviews is better or more valuable than the other, that can cheapen the reason you have for living the way you do
I think the analogy with vegetarianism is apt here because, at least if you take your faith seriously, it places a lot of demands on you, & so the question arises: Why bother? Even if you aren't a convert, there's a lot of social pressure to just give it up as stupid or hopeless.
And so if you're religious, the judgements you make about the lifestyle and worldview of people who aren't religious are going to be intimately bound up with judgements about yourself, about whether the kind of life you're living is really worth it, really worth continuing.
But as Aaron points out, the appropriate reaction isn't just to pretend this isn't so. The real challenge is to try to explain to people what you think they're missing without making them feel like you're dismissing them as they currently are, or treating them as lesser.
