Query uses Primary Key Index instead of Nonclustered index defined
The table only has 2 rows. The cost difference between a table scan and an NC seek is negligible. SQL Server is pretty good about finding the cheapest way to getting things done. I'd expect that when the table gets bigger, the NC index will start getting used.

To compare performance, you can force the index to be used with an index hint:

SELECT lop.RecordID ProspectusID,
    c.c_code CourseCode,
    c.c_desc CourseDescription,
    COALESCE(c.c_major, '') MajorName,
    lop.EffectiveYear EffectiveSchoolYear,
    COALESCE(COUNT(pc.ProspectusID), 0) SubjectCount
FROM dbo.ListOfProspectus AS lop
    INNER JOIN dbo.courselist AS c ON lop.CourseCode = c.c_code
    LEFT JOIN dbo.ProspectusContent AS pc WITH (INDEX(idx_ProspectusContent_prospectusid)) ON lop.RecordID = pc.ProspectusID
WHERE lop.CourseCode IN ('BSIT')
GROUP BY lop.RecordID, c.c_code, c.c_desc, c.c_major, lop.EffectiveYear
ORDER BY CourseCode, EffectiveSchoolYear


In production, I would use the hint as a last resort though. Given proper indexes and statistics, the query optimizer can typically build the cheapest plan on its' own.

Read more about hints: http://technet.microsoft.com/en-us/library/ms181714.aspx