It's too bad you didn't buy the D5100 with at least the 18-55mm VR lens. In a kit I think it only adds about $100. It is a very capable lens and I'm sure your experience would be much different than what you describe. Even though I own a few different macro lenses, I found the 18-55mm lens could focus close enough for some very nice flower photos.
I have the AFS 35mm f1.8 lens and find no focus problems at all on my D5100 or any of my DX bodies.
The only way I think we can help you is to post a link to a couple photos, including full EXIF data, we can evaluate. Of course it's possible your camera has a problem but just about every comment that I recall has been very positive on the D5100. I know my D5100 has been a joy to use and the photos extremely sharp regardless of which lens I use. But without getting into Pro lenses I especially like the results I get with the 18-55mm VR lens.