Well, lexxinski: On the internet, it's almost impossible to tell... One of the big problems with communication over the internet is that you can't see the person you're communicating with, or hear the inflexions in their voice. Words in-&-of themselves don't really give us much to work with in terms of context. So when there is a question regarding a person's intent, about all you can do is ask for clarification.
In person, it's a bit easier because you can "read" the person's face & gestures & hear their tone of voice. But I know what you mean. I have also always been very sensitive to the intent behind other people's statements. And, yes, I would agree that it is closely related to low self-esteem. This is something I have always struggled with as well.
I don't know as I have any particularly great suggestions regarding how to handle situations such as this, other than to "take a deep breath" when you encounter one. Sometimes, if you can just allow some space between what someone says & your response, this can give you time to process what's going on & to formulate an appropriate response.
Of course, you can also simply ask for clarification too. An effective way of doing this, sometimes, is to simply restate what you heard the person say, but put it into the form of a question rather than a statement. So, for example: if the person says: "I think blue is a really dumb color..." you then reply: "Blue is a really dumb color?" This is basically a take-off on a simple counseling technique. "I hear you saying that..." In this way you can clarify what the intention is behind whatever it is the person said. Hope this is useful...