Cycling and running fitness are not the same. Keep your commute up and you will get there. Anecdote. I was contacted through our work cycle group by a woman who wanted to cycle to work but had tried the route she drove but too much traffic. As she lived on my route to work I offered to show her my route in. First day there had been an accident on a nearby motorway which lead to more cars on the back roads I used. I told her it would take 50 mins but it took 1.5 hours as she was not as fit. I thought well she will probably decide to get a lift home in the evening but no she was keen as mustard and rang to check what time to meet to head home. She struggled on the one long hill home and we had to stop three times before we got to the top. But she really enjoyed it and we rode together the next four weeks till she was confident to try it on her own. Our work times did not always coincide. By the end of those four weeks she was able to get up that long hill in one go. Her joy at that accomplishment was a sight to behold. So keep at it consistently and the fitness on the bike will get there.