As you mention Hamas, it gives me the opportunity to point out that Israel bankrolled Hamas founder Sheikh Yassin even prior to the founding of Hamas. This was admitted by former military governor of Gaza Yitzhak Segev and other Israeli government and military officials. Israel wanted to undermine secular political Palestinians and empower Islamist political Palestinians. Once successful, they bemoan that the Islamists they funded and worked to empower, have come to power.
Incidentally, the EU funded NGOs which Israel are spying on here are mostly secular (and even the militant groups which Israel is claiming the NGOs are affiliated with are secular as well).