Aren't Shinobi male ninja and Kunoichi female ninja?
Yes and no. "Shinobi" is simply synonymous with "ninja". It does not specifically refer to only male ninjas. The term "shinobi" is a general term that encompasses all ninja. "Kunoichi" is a subset of "shinobi" which specifically refers to female ninja.
To put it simply, the following statements are true:
1. Naruto is a shinobi.
2. Sakura is a shinobi.
3. Sakura is a kunoichi.
4. Naruto is not a kunoichi.
Think of shinobi as fingers and kunoichi as thumbs. All thumbs are fingers, but not all fingers are thumbs. In the same way, all kunoichi are shinobi, but not all shinobi are kunoichi.