Are Jews and Arabs treated equally in Israel Do they both get the same benefits from Jews specific organizations such as Jewish National Fund ?

Most certainly not.
The JNF itself owns more than 10% of the land in Israel and systematically discriminates against Palestinian citizens of Israel, who make up about 20% of the population, in its allocation. In 2004, following a Supreme Court petition challenging the discriminatory charter of the JNF, the ILA agreed to temporarily open JNF bids to any citizen of Israel, regardless of ethnicity, but if a non-Jewish citizen won the bid to the land, the ILA agreed to compensate the JNF with other equivalent state land. Together with Admissions Committees, the JNF and Israel's discriminatory land policies make it extremely difficult for Palestinian citizens of Israel to gain access state lands for residential, commercial, agricultural, or other uses.
In places like the Negev (Naqab to Palestinians) desert in southern Israel, the JNF has been working with the Israeli government to evict Palestinian Bedouin - who are Israeli citizens - and destroy their homes and communities. The village of al Araqeeb has been destroyed more than 100 times because it’s located on land that the JNF wants to plant trees on as part of its so-called “Ambassadors Forest.”
In occupied Palestinian East Jerusalem and elsewhere in the West Bank, the JNF is also displacing Palestinians, often in cooperation with right-wing settler groups like Elad. Through subsidiary companies like Himnuta, which was established in 1938 to help get around institutional and legal restrictions on its activities, the JNF has acquired thousands of acres of Palestinian land in the West Bank and East Jerusalem, and conducted numerous camapigns to evict Palestinians from their homes to make way for Jewish settlers. Israeli governments have also frequently used Himnuta directly to purchase property in the occupied territories, without going through the JNF, which owns 99% of its shares.