Don't be discouraged!! I had a similar issue. Sorry for the long response but I feel like you need the full story. My son latched fine in the hospital but was very jaundice so I had to pump as well to finger feed extra colostrum. I ended up with damage to the nipple either from him or the pump, we aren't sure which but after the first 24 hours(nursing&pumping combo) it was very painful to feed. Once I got home and my son was eating more it got worse. We met with the lactation consultant multiple times and the latching just wasn't going well. I ended up with mastitis and decided to pump for a few days to let everything heal up. I tried for weeks to get J latching correctly and it didn't work so at around 5 weeks I decided to just exclusively pump and bottle feed.
I was finally coming to terms with it at the 2 month mark and one day J was incredibly hungry and I needed to pump badly(I had waited 2 hours longer than usual). I decided to just try, I mean what did I have to lose right? Well, he latched and is now 3 months and we've been exclusively nursing for a month. PTL!
I never asked anyone, but have wondered if there is a tongue tie issue, his tongue doesn't come out much further than his gums and tends to go back rather than come forward. I think he has probably trained himself (and maybe the tongue tie stretched a bit?? is that even possible?) He also was refusing to even try the breast for awhile. Now he's happier with breast than bottle!
Also if you are pumping and plan to continue, I found that if I tried to stretch the time between pumpings my supply went down, I really had to stick to a rigid schedule. It seemed annoying but I knew my baby was getting the best he could get and that made it worth it. Plus, it really helped to have my husband be able to assist in feedings during those first couple of months. I was sick and exhausted and sometimes just needed to rest.
Don't give up, and remember even if you have to pump your baby is still getting the best nutrition possible, and you can still cuddle and bond just as much as if he were nursing directly. I was so protective of feeding times, the only person other than myself that was allowed to feed my baby was my husband. That was our bonding time with him, and even though I felt a little funny at first I realized that if I was breastfeeding no one else could have that time!