This is a great question. There are a number of things that could be stated. In light of this, let me name two challenges in communicating online.
First, as great as online communication is, there is a limitation when it comes to back and forth responses. For instance, if you are communicating via email or even instant messenger, there is a time lag. You need to compose and then write. Furthermore, the one who is communicating with you will have to do the same thing (in addition to read). When there is face to face communication, people can respond more immediately. This is much more efficient.
Second, online communication can also lack body language. As you probably know, body language is very important in communicating as people catch much more than what is spoken.