As far as I can tell there are no universal rules for indentation. You just follow the style manual/requirements for the work you are doing. And the style requirements for a manuscript do not need to follow the style that the ultimate publication uses. The general principle, if there is one, seems to be that you need to do something to indicate that a new paragraph has begun. So separating block (not indented) paragraphs from each other by spaces seems to be very common in published work. The block style is by far the most common in business letters, and as more stuff is turned out by computers it seems to be taking over from indenting on almost everything produced as a one off.
Manuscripts (really typescripts now) usually are done to a style that requires double spacing, so it is much more common to find indentation required there since an extra space is ambiguous as a paragraph separator. This is also true of a lot of academic writing (theses, reports) where the extra spaces can be used for comments by the editor or teacher. When those are eventually published, often they will be block style.
In any event, the consumer of your writing may have very specific requirements that may or may not be what you learned in English class. If he has his own style manual get it, or if he requires you to follow one of the general style manuals find out which one and follow that.