Formatting is very strict in fiction writing. Crack open any novel, and 99 times out of 100 it will be formatted very specifically -- with paragraph indents. So it's only natural that when you're writing, you automatically hit the tab button as you type along. But you shouldn't, because the tab button is actually the devil.
The Devil in the Details
Yes, the tab button is Satan incarnate. And if you want to avoid a formatting Hell where html code will slap you around with pitchforks, you will never, ever use it when you're writing.
Of course, you still need paragraph indents. The entire celebrated history of fiction formatting isn't going to change just to satisfy your ebooking needs. You can always say to heck with it and use the tabs anyway, but when you convert your work into an ebook later you're going to kick yourself through all 60,000 words (or however many words you've written). That means you've got to think about your paragraph indents from the very beginning -- before you ever start writing at all.
Format your manuscript properly, and it'll be much easier to format your ebook later on. Begin with the blank document that will, one day, become your book. Go to the Tools or the Paragraph section, depending on the word processing software you use, and find the "first line indent option." Change the indent from 0.0 to 0.5. Since you've started with a blank document, everything you type from this point forward will be formatted in this way. You'll never need to hit tab. Every time you being a new paragraph, the first line will be automatically indented.
But it's just possible you don't have that option, because you've already started typing out your story. When this is the case, go ahead and manually remove all the tab indentations in your document. Once this is done, select the entire document and change the formatting using the method described above. Take care of your paragraph indents now, and you won't have to face the devil later.