This behaviour is by design. The idea is that a user is not considered to have enough experience with the topic of the site, so only rep earned on the site is counted: Why is the Association Bonus ignored when trying to answer a protected question?Why is the Association Bonus ignored when trying to answer a protected question?
Part of the boilerplate includes:
To answer it, you must have earned at least 10 reputation on this site.
See also: Improve "Protected Question" message with regard to rep gained through Association BonusImprove "Protected Question" message with regard to rep gained through Association Bonus