There is a difference between "market manipulation" and "illegal market manipulation.

Any action that can impact the price of something can be called "market manipulation". Apple releasing their quarterly earnings affects the price, but is clearly not illegal.

When people short a stock, it is typically because they believe that the current price is not representative of what the business fundamentals and environment dictate it should be. Ie, they expect it to go down in the long run. While yes, the act of "shorting" can lower the price, that is not the main goal of the action, and it doesn't actually cause them an immediate profit (if they wanted to exit their position, they'd have to buy it all right back up, and the price would rebound as they do).