Over the years, I have found that some people are just naturally negative and often employees that are political use criticism as a power structure. This kind of behavior can really hurt a company. Saying no to a project tends not to reduce an employee's stature because the project he or she brings to a halt is never tested. In fact, the employee who says no all the time may grow in stature as they come to be seen as a discerning authority.
Meanwhile, the risks are generally much greater for the yes employee. No matter how many times managers have been right in the past, when they greenlight a project that fails or underperforms, they will inevitably be subject to criticism and, in the political company, the knives will come out.
This is not as it should be. The process of coming up with new ideas is always more useful to a company than shutting down ideas or doing nothing by keeping your head down. Those that criticize experiments after the fact, when more data are present, are not a help to any company. You will succeed neither in life nor business unless you are comfortable trying things out, and selecting the best option available during the period when a decision must be made. Take chances and then move to the best solutions as they become clear to you.
At the highest levels of a company, how a leader handles a project's failure is more important than how he or she manages a success, because it is the failures that determine how much creativity is allowed and fostered within an organization. In my companies, we acknowledge failures and move on. If you are not failing, you are not learning and you are not innovating. Learn from your mistakes, but don't create a culture that does not tolerate risk.
How do you handle people who raise red flags constantly? Make anyone who says no to the a project put forth an alternative that they think is better. If they have no good alternatives, then I'd advise you to fire tomorrow the "no" employee.