At-Risk Youth Protection Act of 2006 - Authorizes the Secretary of Education to make grants to states for subgrants to alternative public schools or programs that serve the needs of students who are at risk of educational failure. Requires subgrantees to require their secondary school students to perform at least 100 hours of community service each school year and receive training or counseling on conflict resolution as a prerequisite to performing such service.
Amends the Internal Revenue Code of 1986 to provide a tax deduction to a business of: (1) $750 per 100 hours of community service provided by such a student through such business during the taxable year; and (2) $2,000 for each graduate of such alternative school or program who completes one year of employment with such business.