The set of assumptions that atheists use are formed primarily due to the *lack* of facts. Scientific method, and all that. "Rabid" atheists, as you seem to be leading in to, like to point out that religious people believe in things with no proof, only faith. So basically, the religious are hoping for something and lying to themselves in the meantime (or at least following the beliefs that one is not supposed to prove or disprove religion, that one is meant to accept it all on faith). Logical people don't like that line of thought.
Yes, this is the line of reasoning which many atheists use and not just the angry ones. At its core is the idea that a religion, almost by definition has no factual basis. Atheist theories hold that religions have their origins exclusively within the human mind or within human societies. The Magical Thinking and Father Figure Neurosis theories are well-known examples. You suggest wishful thinking as an explanation of religion. But theories on the formation and spread of false beliefs cannot all by themselves tell us whether any specific belief system is false.
As I have heard the scientific method argument expressed, it basically boils down to a hope that we will discover natural processes which fully replace God. I believe the best statement of this argument is the following: "It was once widely believed that lightening bolts are thrown by God. Through the scientific method we have discovered the real explanation. In time everything once attributed to God will be reatributed to natural processes." We'll just have to wait and see. For now, this argument has zero persuasive power.
It is not a lack of facts which causes atheists to make the assumptions which I criticised. The purpose of these assumptions is to explain away inconvenent facts. For example, the Bible is a collection of historical, legal, and religious documents which describe what we would today call "contact with extraterrestials". One of them is the "God" in whom atheists would prefer not to believe.
Atheists have spent the last three centuries trying to discredit these accounts. They have done this mostly by making up stuff. They invent imaginary writers who supposedly lived centuries after the named writers. (So that the histories will be historical fiction and the professies written after the fact.) They claim that the stories are mostly folk tales and do not refer to historical persons. Supposedly what we have is the last version of a bunch of documents which each generation hacked to suit its own purposes.
Time has not been kind to these theories. In the 19th and the 20th centuries archeologists dug up the palaces of 'imaginary' kings, found 'fictional' cities, and found objects with the names and titles of even minor government officials mentioned in passing. Meanwhile older and older manuscripts were found which showed that the text had undergone only minor editorial changes. For the Gospels we have partial copies from within a generation or two of the events described.
But, the know-it-alls have not gotten the memo. That is what I meant when I refered to Internet atheists who cite "facts" which don't actually exist. Trying to discredit the Bible with 'truthy' nonsense is a prime example.
I have no beef with atheists in general. But anyone who says that all non-atheists are fools is a fool himself.
Like you I reject the idea that there can be two kinds of truth, religious and scientific. If God does not exist, calling his existance a 'higher truth' does not make it so. If he does exist, refusing to accept it just because "god" is a religious term is similiarly unreasonable.