Though this functionality is not automatic, this can be manually accounted for by using Giving Levels. You can setup a base giving level and then a giving level that includes fees.

Example:

Level 1 - $5 - exclude fees
Level 2 - $6 - includes fees
Level 3 - $50 - exclude fees
Level 4 - $52 - includes fees
Level 5 - $100 - excludes fees
Level 6 - $105 - includes fees

Giving levels can be setup in the following location:
  1. Edit the donation form part
  2. Scroll to Giving Levels
  3. Click Add giving level - enter a name and amount - repeat
  4. When all levels are setup, click Save