"Thinking of you" is something you say for a person to whom you feel exceptionally close and bonded to. Having someone in your life is a great blessing and loving someone feels great. When you are in love or a relationship, you tend to think about your significant other time and again. It is his or her thoughts that you are preoccupied with, most of the times when idle. There is no harm in devoting a fraction of your thoughts to someone whom you love truly, madly and deeply. Rather, it is something that comes naturally to people who are in love.
You tend to think about the other person, his or her thoughts, fantasies and desires. When you are in love you feel like going to great lengths to satisfy the person whom you love. But thinking of someone all the time can be highly distracting and can sway your focus from the task at hand.