Hmm... Is this your first ever bike? Have you driven cars for years?
If yes to both then read on. If no, then probably forget this post!
I can understand exactly what you are feeling if you answered yes to both. I felt the same when I first started riding. Motorcycle engines sound and feel much more "laboured" than car engines. But so long as it is still pulling, and not red lining in the rev counter you are fine.
I found I was shifting up the gears far too early when I first started riding, as I though the engine was making "too much noise" and needed to be put up a gear. In fact, I was just forcing it to be in too low a gear. Bare in mind for many bikes, 1st gear can get you to speeds of 30mph with ease. Riding around a city, 4th gear is probably the highest you want to be in, I normally stay in 3rd.
When I took the new cb500f out for a test ride, top gear was only ever used once I had reached 70mph and was cruising along. Tended to stay in 4th or 5th until then. I did find the exhaust uncomfortably quiet to be fair, especially when up to speed. I do wear ear plugs however so that would have been dulling it even more.
As Blipco suggests, try dropping down a gear, or not shifting up them early and see how you get on. When you twist the throttle, even slightly, the bike should pull with ease. If it doesn't then you are in too high a gear for your speed/terrain.