I wondered about that, too. But after reading some articles, yes, they can be used for the Athletic Dept.
Here's Alabama's explanation:
http://www.rolltide.com/sports/crimson-tide-foundation/spec-rel/content/faq-endowments.html
Can I restrict the use of an endowment?
Within reason, yes. Donors may restrict the use of funds from their endowments to support areas such as scholarships, programs, facility maintenance, coaching, etc. And, more specifically, for a particular sport such as football, gymnastics, Olympic sports, etc. If this is of interest to you, please contact a member of the development staff for more information about what your available options.
Are there minimum levels to endow a fund?
Yes. Depending on the type of endowment being established, minimum endowment levels are set by the Crimson Tide Foundation Board of Directors and are as follows:
Endowment Minimum level
Athletic Department Operational Fund $500,000
Head Coaches' Championship Performance Fund $100,000
Bryant-Denny Stadium Maintenance Fund $50,000
Coleman Coliseum Maintenance Fund $35,000
Named Endowed Athletic Scholarship Fund $25,000
What is considered to be a fully endowed athletic scholarship?
Given the current cost of tuition, we consider a fully endowed athletic scholarship to be $300,000.
Also, this:
Athletics: Some alumni and donors make charitable endowment gifts for the restricted purpose of supporting intercollegiate athletics. Colleges and universities use investment income from such gifts to fund athletic scholarships, facilities, salaries and equipment.
http://www.aplu.org/NetCommunity/Document.Doc?id=577