The Biggest Myth Of The Syrian War Is That The Rebels Are Dominated By al Qaeda
Zelin estimates that there are 5,000 to 10,000 fighters comprise Nusra, which wants to establish an Islamic Caliphate in the country's north.

Zelin, who tracks jihadist groups extensively, estimates that 5,000-10,000 foreign jihadists have arrived in Syria and that about 1,000 have been killed in the fighting.

O'Bagy estimates that supporters of Jabhat al-Nusra and ISIS — the two main al Qaeda-linked groups — probably involve about 5,000 to 7,000 fighters while the number of rebels participating in offensive operations is about 80-100,000 rebels.

So a subset of Syrian rebels are certainly linked to al Qaeda, but terrorists only make up about 10% to (at the very most most) 20% of the opposition.
http://www.businessinsider.com/syria...l-qaeda-2013-9