Yeah, that's normal. 0 is the tile for coffins in game, so you'll have to bear it if you want a graphics set.
No longer! (though thanks Spacefox, it seems to have been this feature of your excellent set which prompted the flood of awesome plugins
You may be interested in the new
Text will be Text plugin, which allows you to set up a separate tileset for text to the rest of the tiles. As of version 2.01 (2014-06-04), it also allows you to add an arbitrary number of additional tilesets, tiles from which can be set to override specific items or building tiles. This functionally implements eternal suggestion #4 for full graphics support.
I'm going to include this in the Starter Pack, and it would be great to have a 'pure text' version of your tileset that can be dropped in. Most of the letters are already clear, but there's a few things like the quality symbols and any changed letters, numbers, and punctuation which are hopefully easy to include in a pure text tileset, and would make things a lot easier to read in cases where truetype doesn't work or has been disabled.
Any further stuff like overrides would be awesome, but given the rate of updates (including recently a demo of allowing different tile width for the menu) you might not want to invest too much time just yet - but don't let anyone stop you if it look fun! It's also probably a good way to deal with the whole walls-as-leaves thing that's going to come up in the new version, though that's still not so bad as the cursor/stairs/bins/'x' mixture.
Please don't feel any pressure - I just thought it worth sharing with the people who have done the work to make pretty graphics happen already