Why do they think this?
I can think of a few intertwined reasons why the students think that $-x$ is negative.
Firstly, psychologically the $-$ sign has a very strong pull towards thinking of subtraction and negative numbers. When they were small, your students had more than five years to get used to the idea that $-$ meant subtraction and that subtraction always made things smaller. Then on top of that they probably had a few years to connect $-$ to negative numbers before they were ever introduced to letters representing numbers. Those instincts were forged very strongly and are still stronger than anything that came after, so when they see $-x$ it is natural for them to think of negative numbers.
Even more than that, their first and most strongly-forged experience of numbers is the counting numbers, and that will always be the first thing they think of unless specifically directed to think otherwise. If you ask any person -- even a mathematician -- to name three numbers I daresay they will pick three positive whole numbers. They won't even pick 0. In fact, in my experience, 0 takes up a very small amount of mental space and is often forgotten as an option in all sorts of situations.
Secondly, over in other courses like economics and chemistry, variables usually do represent positive amounts and graphs only exist in the first quadrant, so it is not unnatural for that thinking to transfer over to maths.
Finally and most importantly, I don't think that your students think of the $x$ as standing for a range of possible numbers at all most of the time. I'm pretty sure you don't either. If you really analyse your own thinking, I'm pretty sure you find that when doing algebra, you mostly think of $x$ as an object of its own kind that moves around the page, rather than a number at all. You can substitute numbers in its place, sure, and make a statement that it is equal to a number, sure, but they are not the same as actually conceiving of it as a number at all times.
What can you do to prevent it?
It would probably be a good idea to review the classic functions and their behaviour early in your calculus course -- you probably do this anyway. What you can do to help yourself later on is to focus explicitly on reminding students that $x$ (or y or t or whatever) represent various numbers and that one way to understand a function is to ask yourself about what happens when $x$ is various possibilities. Basically this is considering the domain and range of the function, which you probably also discuss in your calculus course anyway. You can tell them that domain and range are not just information about the function that they need to be able to find for tests, they are a fundamental way of understanding functions.
As the course progresses, reinforce this idea: every time you write down a function, take a moment to consider the various x-values that could go in and the various function values that come out. (I'm not saying calculate the domain and range formally, just take a moment to think about it aloud.) I recommend asking "Can I put in 0? Can I put in positive numbers? Can I put in negative numbers? What about very small and very big numbers?" If they are used to this happening every time, they are more likely to do it themselves and come up with the idea that $\sqrt{-x}$ is ok by subbing in $-2$ on their own.