There is a group of about 10% of voters who are firmly independent( http://www.gallup.com/poll/15370/Party-Affiliation.aspx )
Whoever the Republican nominee is, they must win over 50% of the independent voters in order to beat the Democrat nominee.
Trump has very high unfavorables, especially among independents, which is why Cruz barely beats Clinton in the match-up polls while Trump loses.
It’s simple math.