Why is it difficult for employees to express hatred to their boss? Suppose Bob hates his boss. Note that Bob is an "average" person. Also suppose that he shouts as loudly as possible "[Curse] my boss" (with nobody else around but him). 

Why is it so difficult for Bob to say this directly to his boss? Is this based on social norms or is there a specific brain region which restrains this outburst?
While there may be many social norms operating that discourage expression of hatred to your boss, typically there would be many rational reasons not to express such hatred:


The employee's job could be terminated, which may result in lower income for the employee or  a worse job in the future. Swearing in the workplace would often be considered harassment which would often be grounds for termination.
Even where an employee has arranged another job to go to (but then technically, the relationship is not really one of employee to boss), there is the risk associated with reputation damage that can result from verbally abusing a boss.
If the outburst does not result in loss of job, a boss typically has extensive control over the employee. Bosses can typically influence your work duties, when you get leave, when you have to be at work, whether he supports a promotion, who is terminated during a redundancy process, etc. If your boss likes you, then they often have substantial discretion to make your life easier. In all those kinds of situations, life is easier if your boss is on your side.
Independent of the power relationship, you need to spend time with co-workers, and many people find it more pleasant to exist in a pleasant social work environment.


Thus, I don't think we need to resort to a neural explanation to adequately understand this behaviour.

Furthermore, presumably there are legitimate ways of expressing displeasure with your boss that would be more effective in achieving your goals. This might broadly come under the heading of "negotiation".