I think the first thing to say about this is that it’s always acceptable to avoid these abbreviations... even in the shortest, most intimate SMS or instant message, a fully-spelled-out *you* or *are* would never be seen as too formal.

That being said, if you are worried in the least that the person who you are corresponding with might think you are stupid, uneducated, or inappropriately informal, then using “u” or “r” in communication will give them an easy reason to believe that you are.

I would say I personally never use them, but that would be a lie. Sometimes in very hastily composed text messages on my phone I will take such a shortcut. But if I have a full (real) keyboard at my disposal and no 255-character limit, then there's no excuse for such sloppiness.

On the other hand, if your correspondent is using them there’s no reason other than personal pride why you shouldn’t use them back to facilitate the conversation.