There is no negative bonus, just as there is no positive penalty.
This is actually spelled out explicitly for ability scores in the text. From the PRD, under ability scores:
Each ability, after changes made because of race, has a modifier ranging from –5 to +5. Table: Ability Modifiers and Bonus Spells shows the modifier for each score. The modifier is the number you apply to the die roll when your character tries to do something related to that ability. You also use the modifier with some numbers that aren't die rolls. A positive modifier is called a bonus, and a negative modifier is called a penalty.
Under combat, Armor Class, there's is also this clarification:
Sometimes you can't use your Dexterity bonus (if you have one). If you can't react to a blow, you can't use your Dexterity bonus to AC. If you don't have a Dexterity bonus, your AC does not change.
Which means that you lose your dexterity bonus when surprised, but you do not lose your dexterity penalty.