By default, the InDesign preference General > Always subset fonts with glyph counts greater than is set to 2000 characters. However, there are many popular fonts that have many thousands of glyphs beyond that and changing this number to a higher glyph count to accommodate those fonts does not work. The fonts are still subset even if the PDF export setting is set to "Subset fonts when percent of characters used is less than 0%."

Fonts to try:
Garamond Premier Pro
Arno Pro

This is a major problem for files intended for print that require fonts to be fully embedded.