Two things will help:
(1) Apply paragraph styles, cell styles and table styles.
(2) Use the latest version of InDesign, preferably InDesign CC 9.2, the latest upgrade. With each new version, EPUB export of tables has gotten better.
We need more details to help you out here. Could you please explain what attributes you wish to be preserved in tables while exporting to EPUB. Which version of Indesign are you using?