What kind of programming are you interested in? Do want to learn shell scripting (such as bash, csh, ksh, etc.) or Perl or C/C++ or Java or what? If you are interested in specific languages, the syntax is independent of the operating system. Of course, you need to learn the tools that are available to compile and debug programs you write. So is this what you need help with?
With that said, I found that "Beginning Linux Programming" from Wrox Press was a good book for an introduction to shell scripting and the tools available for programming in C and C++ under Linux. It also provides an overview of GUI development with X. Much of the book is also applicable to other Unix variants.
If this isn't what you are looking for, please be more specific about what you want. I might be able to come up with some other suggestions.