Starting with version 2.1, the GoMage Feed Pro extension has a "Product Type" attribute. Now you can use the following method to add only configurable products to the feed file:
Screenshot: Adding Only Configurable Products
Method for older versions
1. Go to Catalog → Attributes → Manage Attributes and add a new attribute (for example: Product Type, product_type, add value 1).
2. Go to Catalog → Attributes → Manage Attribute Sets and add the Product Type attribute to Attribute Groups for (all) your Attribute Sets.
3. Go to Catalog → Manage Products and mass-update attributes. Set 1 in the Product Type field for all specified products.
4. Go to Catalog → Feeds → Manage Feeds → Filter Configuration and set the "Product Type" attribute equal 1.