There are certain misconceptions about the scientific method. One of the most usually claimed is that science, too, depends on blind faith. On the contrary, the only "faith" that exists in science is that the Universe has some laws governing the reaction between matter and energy, and that we, as humans, are able to understand it. Apart from that, as stated above, any unwarranted claim is met with a demand for evidence -natural, observable, objective data. Every formally defined system -including mathematics, heavily used in science- contain some axioms, but these can be regarded as more of definitions that assumptions.
Another false impression is that scientists are a group of back-patting individuals. This is simply not true, as there is a quite high level of competition amongst them. This is, of course, not a problem with the method per se, but rather human nature, which is unrelated. In fact, it is useful, as it speeds scientific advancements, while, unfortunately, leading to some occurances of fraud. However, those are generally uncovered due to scientific rigor, peer reviews, and the like.
A gross -and, sadly, quite common- misconception has to do with the meaning of the term "theory". Some believe that it is a synonym for "assumption", while, in science jargon, it is an explanation of the facts. The facts are objective, while the theories attempt to link them and find relations between parameters. The colloquial use of the term differs, of course.
Moreover, indoctrination and conformism really have to do very little with science, since it is simply a tool to understand the world around us. Going against a well-established theory is not anti-conformisting nor intellectually meritable, unless one can provide rational or empiric warrants.
Lastly, some persons regard science and scientific laws/theories to be prescriptive, meaning that they are supposed to provide a moral framework of some sort. On the contrary, scientific laws are descriptive, dexcribing reality in the most accurate way possible. They document cold, hard facts and the causes of phenomena. While it is true that such scientific conclusions can be used to further an agenda, that is not their purpose.
Long story short: science was basically born the day a philosopher called Archimedes woke up and said, "OK, guys, stop binge-eating and philosophising; we COULD get out and see if we're correct, right?" (I love to joke about my ancestors) He did not follow his own advice, but it was a start, with Galileo, Newton and then Einstein and all the modern scientists following, adding to the definition of the scientific method.
Science is all the above. It is not a religion, an ideology, a doctrine, a belief system or a faith. It is an empirical inductive model to arrive at conclusions regarding the laws governing the Universe. Nothing more, nothing less.
And, one last thing; I implore you, never, ever confuse the scientific method with the applications of it. Never.
There have been frauds, of course; how about the scientist who claimed that he transplanted black rat's skin to white rats, only for a cohort of him to discover that they were... painted? Scientists are not gods; nobody has ever claimed that -rather, some claim that scientists claim it. To play God is to alter nature, not discover its laws. Again, this is a confusion of technology and science; related, but different.
There is no indoctrination; you cannot indoctrinate someone with empirical facts, neither the description of theories. Finally -and a late thank you to anyone who bothered to read this wall of text-
religion and science are only enemies when one of them swims in the other's waters -that is, when scientists try to derive conclusions about what we should do, and when theologists claim entities that CAN be falsified, and therefore are in the realms of science. Scientists answer WHAT, WHEN, and HOW. Religious people -or philosophers, for that matter- answer WHO and WHY. Stick to your job, people. As long as you don't get in the way of the other search party, we'll all be fine.