Saudi Arabia is a Daesh that has made it. (Source)
To what "has made" refers? To what "it" refers?
As Don B. and David Siegal point out, "has made it" means "has made the big time" or "has achieved great success". Daesh's other self-proclaimed names state the level of success it aspired to:
The Islamic State of Iraq and Syria (ISIS) or The Islamic State of Iraq and the Levant (ISIL). In this context, a "state" is a sovereign government that can wage conventional war and make peace, and interacts as a more-or-less equal to other sovereign states in forums like the United Nations.
A caliphate. A caliph is a pre-eminent Muslim ruler.
The House of Saud started about 275 years ago as a deep-desert tribe with a radical theology.
The Kingdom of Saudi Arabia started as a platoon of cavalrymen who raided a fortress in Arabia about 120 years ago. Over the next 30 years, it grew to control Mecca, Medina, the rest of the Hejaz, and most of the interior of the Arabian peninsula.
The Kingdom of Saudi Arabia is a sovereign state. It is a member in good standing of the United Nations. For purposes of diplomatic protocol, it is treated as an equal by almost every state in the United Nations.
The king of Saudi Arabia is the most important Muslim monarch in the world today. Control of Mecca gives him the ability to publish official versions of the Koran. Oil wealth allows him to sponsor mosques around the world that promote the Wahabbi theology of the founders of the House of Saud.
It is therefore reasonable to conclude that the Kingdom of Saudi Arabia has achieved a level of success that Daesh aspired to.
Here is an attempt at a partial answer. When I say a person "has made it," I mean they have achieved a level of success in what they're doing. For example, if I had a friend who played baseball, and he became a major league baseball player, I would say, "He's made it." The "it" you are asking about refers to whatever success the subject has achieved. In the case of this article, it's hard to say. I could only read a couple of paragraphs of the NY Times article you linked to. The author appears to be making an unflattering comparison between ISIS, the terrorist organization and the country of Saudi Arabia. I would have to be able to read more to give a better answer.
In general, to say that "X has made it" means that X has achieved a significant level of success.
In the particular case of the linked article, the author is saying that Saudi Arabia is similar to ISIS in its religious and cultural beliefs, and in encouraging Islamism and jihad-ism but that Saudi Arabia has "made it" in that it gets favorable treatment from the West, even formal alliance, with its religious and cultural oppression of its own people and of others being overlooked or denied by the West, because it is too prominent and useful to challenge.