What does "Can I help you?" really mean?

Question

I am a non-native English speaker. Whenever I travel to the States and I sometimes hear the question, "Can I help you?"

At first, I thought it was a sincere eagerness to help me. However, after a few incidents, such as accidentally entering a wrong meeting room once, I learnt that this question can also mean, "I don't understand who you are or what you are doing here."

So now I am confused if there is also a negative connotation associated with this question and if there is, then how do I understand from the context if this question is asked positively or negatively.

Are there any thumb-rules one can follow to deduce if "Can I help you?" is said in a positive or negative way?

Answer 1

I am sorry that my answer has to be long.

If asked this question, it is helpful to think about on whose territory you are and why.

In an open shop you are on territory where your role is to buy, theirs is to sell; you may safely assume that they want to help you buy.

On a public street you are entitled to be there and if you looked puzzled you may safely assume a genuine offer to help you find your way.

If you are on private ground they may ask you the same question with the same helpful intention (you may merely have lost your way), but there is also the possibility that you have entered the ground with purpose; you must recognise that you are not entitled to be there and should take the question as an invitation to leave, or to establish entitlement (“Yes, I understand from your advert that you want to sell your car”). Otherwise, apologise and leave.

Similarly, if you enter a room where a meeting is taking place, The question implies that you must recognise that the room is territory where you are not expected or entitled. Only with good reason (“yes, I am here to tell you the hotel is on fire”) can you establish entitlement. Otherwise, apologise and leave.

Answer 2

Anton's answer already contains all the practical advice that anybody may need on how to react to this phrase, but for the purposes of this site it should be clarified that, when the phrase is used in the circumstances that the OP finds problematic, it has exactly the same meaning that it has otherwise. What connects this use of the phrase with its ordinary meaning is the chain of reasoning that, if made fully explicit, would go like this:

This person obviously doesn't belong here, but he looks like a nice guy, and not like somebody who is intent on doing mischief, so it must be that he entered this room by mistake, while looking for another one (or, at least, I'll give him the benefit of the doubt and assume that this is so). I'll therefore offer to help him to find the room he is looking for (which will, incidentally, also be the most efficient way of getting him out of here, so that we can continue doing whatever we were doing before he came in).

Even in these circumstances, the question thus is an offer to help. It is, of course, quite possible that the attitude behind the question is not one of pure helpfulness, but also involves annoyance, suspicion, and the eagerness to be able to get on with the business one was engaged in (much will depend on how prominent the parenthetical parts of the above paragraph are in a particular case), but that does not mean that the phrase itself was anything but an offer to help.