Conflict in the work place is not necessarily a bad thing.  Debates, fresh ideas and alternatives concerning various work related issues can bring about innovative solutions.  The problem of conflict is often in the process not necessarily due to the disagreement of handling the issues. 

Employees may be disheartened in disagreeing with peers or superiors since past conflicts resulted in unpleasant results.  The unpleasant results  vary from being constantly beaten down, or ends up in emotional turmoil.  The process must include a professional atmosphere and attitude along with a strategic thought process.  Emotions should take a back seat in the process.  Home work should be done to back up suggestions that may counter the current trend.  Build on areas were there is agreement and build your case from there.  It is easier to begin a debate from common ground then go into areas of controversy then to jump right into conflict.  Listen to the other opinion.  There may be merit in truly understanding the opposing point of view.  Be willing to compromise creating a solution that contains both sides of the argument.