I have heard that when done with the book, I still won't be able to program in Python. Can you elaborate on that?
Also, what do you recommend after completing your book? I'm interested in building web apps.
When you're done with the book, I say you can't really code yet because you lack experience actually using Python. You have all the syntax and tools, you just don't really know how to apply them. What I recommend now is you go through the Django Book 2.0 and do all the code in that book. Once you do that you'll have enough to start building your own stuff.
I'd also say, whatever you make will probably suck for a while, but that's alright. Just keep making stuff, put it out there, get feedback from good coders, and improve.
Be careful about whose advice you take. There are a lot of programmers out there who are so far down the road to perfecting their craft that they can't see where they started.
For a mature programmer, using powerful tools will aid them in expressing their complex ideas quickly. As a beginner, you'll experience a ton of "ah ha!" moments where an idea will come to you in code, rather than in abstract. It will start simple with data structures like dicts and will progress toward object-oriented structures.
To say you won't be able to program when you finish LPTHW is to say that a 5th grader can't write. They're not going to write "The Great Gatsby", but they can write.
As per the Windows vs Linux debate - I have found most physics labs use either various Linux distros (Red Hat is super popular) or OSX. I myself have a MacBook Pro running OSX and so I just downloaded and will be using TextWranger as an editor to complete the lessons.