Old question, but still an issue. I had searched for a solution myself but after reading this and other sites saying no, it can't be done I gave up. Then by accident I discovered how to change them :) You are limited to what pictures you can use, and any bookmark that already has a picture of the company logo will not change.
Open a safari page.
Tap on the bookmarks icon.
Tap favourites.
Tap edit.
Select a bookmark with a generic letter-in-a-cube pic and tap at the start of the name.
Switch to emoji keyboard and select a relevant pic.
Tap done!
Here's a before and after shot of my favourites screen so you can see what I mean :D