I have been retired for the last 2 years, and in the summer month cycle about 30 miles every other day. I have lost and kept off about 20 pounds. I have type 2 diabetes and take tablets to control it. When I ride my A1c drops to about 6.1. There is no doubt in my mind that cycling is extremely healthy.
Now to the point that will get some discussion Im sure. I ride a LWB recumbent. Personally I believe it to be a far superior way to cycle. Since there is no pain associated with bents there is no damage to the body. I disagree with the thread about calicum loss because on my bent I do load my legs between the seat back and the pedals. People with several physical problems can cycle on a bent. People with back, neck, arm. wrist, and hand problems find that they can ride a bent with little or no pain at all.
There is no comparison between cycling and exercising in a gym. The gym is totally boring, while riding my bent setting upright I can view the road and surrounding. In a sched amout of time I can travel a fairly long distance with many different routes which lowers boredom.