What to do when you head tells you one thing and emotions another.

Ok, so im pretty embarrassed to even have to ask about any of this, because logically I know the answer, but it’s like somewhere emotionally, I dont want to. Because of that I dont know what to do. The situation is, at work, there was this person, right from the beginning, he was really flirtatious with me at times then he would be friendly but more professional and it would go back and forth..and I just never knew how to read it, I never knew if he was one of those people who were super friendly and it was miscommunicated as flirty or if there was some part of him that was being flirty. I kind of put it out of my head, because 1. he had a girlfriend he lived with and a baby who was like 9 mths old or so..and that was a whole bunch of “baggage” I did not want to get into with anyone. Then as time progressed I learned that him and the girlfriend are splitting up, he is moving out, he has feelings for me etc etc. I really cared about him…however. I was really skeptical about letting that be something that was open, because I’ve been burnt a lot in the past, like a lot of other people..and I felt like with a guy who just got out of a long term situation with some girl and has a kid..im not going to get my hopes up just yet…but somewhere inside..after hearing all these really nice things that I have been desperately wanting to hear from someone, coming from someone I would never imagine would take an interest in me, there was a part of me that did get excited, and thought that maybe I could be really happy and maybe it was my turn to have a really good relationship, and what he was saying to me was all really true. time went out..we hung out more and more..things were going really well but we decided it was bet to keep things quiet about each other at work… one night we got together..and he left his car in the parking lot at work.. I was bringing him back when out of nowhere..the boss/owner who lives near by drove by and pulled in the lot because he saw lights on in the building that hadnt been shut off.. I had been pulling out..he knew my plate numbers and the jig was up. Since then..things have been going downhill steadily.. at first, this guy said we would have to just be more careful and secretive..to where now..about a mth later..we barely talk..he says nothing will ever happen between us..and its better that things are this way because we work together and it wouldnt be right. may I add that the boss/owner told him that he should keep it just business may I also add there is no policy against any of it.. I feel awful it sucks to see him at work everyday and talk to him every once in a while and hear him say that yes he misses me, yes he still cares but no nothing will ever ever happen.. I just dont understand how you can say all the things he said to me, sleep with me, and act like we are going to have this great relationship..and then because someone says…oh you should just keep it business…decide..that person is right] because that person has had bad luck with woman..even though that person is dating an employee..what the f*ck..thats so hypocritical.. what do I do..??? how can I stop feeling so let down?