A number of sources in WWE have said that the voting was 100% legitimate. The winners were who the fans picked.
The Superstar of the Year vote was extremely close and yes, there are people in the company who are pointing out that while Daniel Bryan won the fan vote but wasn't considered enough of an "attraction" by Vince McMahon to be given a run with the WWE Title. That decision looked like a huge mistake at the time and even more so now.