I think it goes beyond implication though. There are conditions by which a reasonable person can be expected to understand that saying "I'll pray for you" is offensive, even if there is no direct intent to insult. And generally, those conditions are the same conditions that prompt people, who are likely to say such a thing, to say such a thing. So effectively, if prayer was not directly solicited by the target of the prayer, I rarely see cases where someone says "I'll pray for you" where it isn't either a direct insult or indirect offense.
There is a big difference though between "I'll pray for you" and what we're talking about int this thread, i.e., the assertion that certain things are myths. In a discussion, different perspectives are expected. So if an assertion is made "X is true because (for example) the Bible says so," then a counter-assertion, "The Bible is not a valid premise for an assertion of fact because it is a myth." How does "I'll pray for you" constitute a substantive support for any assertion? It isn't part of any discussion of issues.
This works both ways, though: Just jumping into a thread and telling someone that their beliefs are myths, without the context of those beliefs being used as justification for actions or foundation for other assertions, is also inappropriate.