What does "terms" mean in the following sentence?
But I believe the theory of a creator of the universe can be explained in rational terms
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"Terms" is being used here in the sense of "expressions" or "propositions". The writer is declaring that his theory can be expressed in such a way that it can be tested by rational argument as distinct from the usual emotional shouting-match. This does not necessarily mean that the writer's theory is true, though from context the writer clearly believes that it is and expects that a dispassionate rational analysis of his argument will support him.
This 'terms' is from the same origin as 'terminology' - i.e. the words and definitions used to describe a topic.
Rational terms is an idiomatic phrase, and breaking down idioms into their constituent parts is rarely a productive exercise. That said, "terms" is more or less a synonym of "words", and "rational" can mean "not confusing, logical", so in this case you can actually arrive at something resembling the actual meaning by looking at the parts: in rational terms = using logical words (as opposed to emotional or politically-charged words or legalese or any similar obfuscation).
This means that the theory of a creator of the universe can be defined in such a way that everyone can agree upon. So 'rational terms' in this case would be those definitions that everyone can agree upon.
Now, whether that's true or not is completely subjective.