For some reason short-selling has a bad reputation in many circles. It is often blamed for bad things happening to good companies and/or good countries. The story among short-sellings critics is that it involves market manipulation, where big actors are attempting to profit by sending stocks or bonds plummeting.
Floyd Norris has a good column on short-selling in today's NYT. It sums up research on the issue which indicates that most of the time when companies are complaining about short-sellers, the shorters are actually identifying over-valued stocks and in some cases uncovering fraud.This certainly seems to have been true of the short-sellers who were attacked Fannie Mae and Freddie Mac before they were put into conservatorship or Lehman, Citigroup and other badly troubled banks in the heyday of the financial crisis.
Certainly there are instances where shorting is in fact market manipulation, but there are also instances where traders take long positions to manipulate the market. (The notion of market manipulation here is using your trading to deliberately drive stock prices in the hope of being able to profit from the movement you have created. In the case of shorting, you hope to send the stock price plummeting and then buy back shares at a big discount. On the long side, the hope is to create a euphoria around the stock and then dump it before people realize that the price has no basis in the fundamentals.) There is no intrinsic reason that short trades will be more susceptible to manipulation than long trades, except that most small investors (who lack the ability to move markets) can't do shorts.
Short-trading, when it is based on fundamentals, can be seen as equivalent to exposing counterfeit money. It is showing the public that a company is not as profitable as widely believed. It would have been hugely beneficial to the economy if we had many people shorrting Lehman, Citigroup and the other companies pushing and securitizing subprime mortgages back in 2004.