This is not necessary that they only provide Scholarships to Muslim students only. Some of them provide Scholarships to other students also.
Government Scholarships for Muslim Students:
Government of India: http://minorityaffairs.gov.in/
West Bengal: http://www.wbmdfc.org/
Uttar Pradesh: http://minoritywelfare.up.nic.in/
Rajasthan: http://sje.rajasthan.gov.in/
Pondicherry: http://socwelfare.pondicherry.gov.in/
Orissa: http://www.orissa.gov.in/
Madhya Pradesh: http://www.mp.gov.in/
Kerala: http://www.collegiateedu.kerala.gov.in/
Himachal Pradesh: http://www.himachal.nic.in/
Gujarat: http://sje.gujarat.gov.in/
Goa: http://www.goasocialwelfare.com/
Delhi: http://www.scstwelfare.delhigovt.nic.in/
Chandigarh: http://www.chdeducation.gov.in/
Bihar: http://minoritywelfare.bih.nic.in/
Andhra Pradesh: http://apsmfc.com/
Scholarships from various Organizations:
www.imef-ub.org
http://www.iiccentre.org/
http://www.wbmdfc.org
http://www.sit-india.org/
www.muslimhands.org
http://www.metdelhi.org/
http://www.mp.gov.in
http://www.karmin.in/
http://www.isdb.org/
http://www.iosworld.org/
http://www.hashmitrust.com/
www.fscwecare.org
http://www.faeaindia.org/
www.danishtrust.co.in
http://www.childrenfoundation.net/
http://www.wbmdfc.org/wakf/index.html
http://www.bsazakaat.org/
http://www.aaane.us/
http://www.aligs.org/
http://web.mit.edu/
http://www.akdn.org/
http://www.gsr.pdx.edu/