For such cases, FontCreator would not generate negative values either if there was an option to exclude positive values. As noted above, there may be some cases where manual adjustment is required after auto-generation. The automated process depends on the shape of the glyphs and the white space between them.
What value are you using for the Glyph Spacing with auto-generation?
Take a look at Adding Subtables for Kerning Lookups, which makes it quicker to find and adjust manually those pairs that need it.