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HTML -- Hypertext Markup Language. HTML only gives web browsers instructions on how to display pages. It cannot make calculations, do loops, or perform most tasks that actual programming languages can.
By Java, I assume you mean Javascript. Java is a complete, cross-platform programming language that is not used on web pages, while Javascript is a scripting language commonly embedded within HTML files.
The difference, now, should be apparent. Javascript can take input, process it, and give output. HTML can only output. To get a better idea of what each is used for, as well as how to use them, do Google searches for "learn html" and "learn javascript."
If you are going to design a web page, you will definitely need HTML, may need Javascript, and certainly won't need MS Publisher. If your page will need to be very interactive for users, I suggest PHP (again, Google) in place of Javascript. MS Publisher is probably not the correct Microsoft product for designing webpages--I believe the right one is FrontPage. Regardless, FrontPage has a nasty habit of making code that only works in Internet Explorer. It probably also restricts, due to its design, what you can actually place on a web page, while skill with HTML will let you do everything FrontPage can do, and more.
Since you're a user of the internet, learning HTML, Java, and perhaps some PHP wouldn't be a mistake. It's a lot like learning to speak the language when you move somewhere.
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