Well, it all depends on what you want to learn. Many programming languages have their roots in Unix, and that means that the basics of the language usually work immediately. What I mean by that is that until you get to more advanced programming, there shouldn't be many Unix-specific tricks. C is Unix's system language, BTW, and much Unix software is written in it. But you can write applications in C, C++, Java, Perl, Python, Ruby, Fortran, Objective C, Smalltalk, etc., ad nauseum.

If you're interested in GUI programming, that's a whole different story. Unlike Windows, there are multiple GUI APIs, and they bear little similarity.