What you describe (religious people giving bad ratings) is a fundamental problem with one dimensional systems. They just won't work as general purpose reputations which are certainly multi-dimensional.
An ebay seller rating can be one number because it pretty much just means "Does this person send what they posted".
But a general reputation covers so many things. The solution is probably a bunch of different ratings, maybe connected or maybe not.
The ultimate answer probably looks a lot like no answer at all, people just making connections and vouching for each other to make new connections. Tools for finding paths of trust of arbitrary types types would be nice. I have a great reputation without being involved in any official reputation systems at all.
I'm thinking about the one-dimensional system based on "does this person obey his contracts". I think it is central to reputation. And everything else can be based on it using freedom of contract.
I acknowledge that there are a lot of different things reputational systems can be used to evaluate. But they are not worth much without the central one. You may be highly competent in every question - if you are a cheater and a liar, it is dangerous to cooperate with you. The stupid but honest guy is, then, preferable.
Ok, there may be some aspects of honesty - imagine some Muslims who consider everybody else except Muslims as fair game for cheating. Other Muslims, then, may be interested in another type of reputation - "Muslim honesty": "does this person obey his contracts with Muslims". But this "Muslim honesty" can be organized in a system which focusses on a single general honesty - the Muslim creates two identities, one honest which makes contracts only with Muslims, and the other one for contracts with other people.
So I would say, reputation for obeying contracts is special for human cooperation, and deserves special treatment. A reputational system should be, therefore, centered around this special question. If there is a reputational system which is optimal for this question, it is preferable.
Then, of course, one can think about extending this system of reputation to other questions. If this makes sense, fine, if not, one has to design other reputational systems for these other questions.
In other words, the reputational system has to be as good as possible for this single question, everything else being secondary.
Why this question is that special? The point is that we can consider society as a large network of contracts. Such a network of contracts can be modelled in the net, using, electronic (Ricardian) contracts. Seeing these contracts, programs may evaluate them and extract a lot of useful information - but all this information is useful only if we can rely somehow on the reputation of the participants. Contracts and promises made by cheaters are worthless, anything based on it is worthless too. So, whatever we want to do online about contracts depends on this particular type of reputation.
have an electronic system of