Someone recently told me this little gem, which I think may be helpful to a starting programmer...
Always charge the greater of a) what you need to make to live or b) what you're worth.
It's really quite true. If you have extensive programming and design skills, asking for $100 / hour is not unheard of - especially if you can deliver a value of $100 / hour.
On the other hand, just because you're starting out, doesn't mean you need to charge min-wage. Remember (at least in the US) that taxes, and other expenses mean your real wage is about 50% of what you charge. If you charge $25 / hour, you're really only taking home about $12.50 / hour, which is only about $26k / year. If you can live on that, fine. But most people need between $40 and $60k / year. Backing into that, an average programmer should be charging $40 - $50 / hour for freelance work.
That said, and to answer your original question, you should consider everything you do in a project, and determine how you want to bill. Remember, 25%+ of the project is going to be just communicating either via email, IM or phone. So make sure you account for that. You can either itemize every little thing you do and bill at different rates, or you can do a flat fee rate for everything.
I can tell you that if you charge $x for programming and $y for html, you're going to run into trouble down the road. Because some people will say "why is this charged as $x and not $y?". IMO, it's better to charge the same rate for all your work.
Hope this helps.