Where do we start. Well first, what do most people mean by "the scientific method"? Well no doubt, most people don't have a clue, they just try to make appeal to the authority of science, without really understanding what it is.
But by and large what they are referring to is "inductive reasoning". - In contrast to deductive reasoning (which dominated science since Aristotle) inductive reasoning is testing and refining hypotheses by observing, measuring, and experimenting. It was systematically introduced to "science" in the seventeenth century by Francis Bacon.
Now the problem is in theoretical physics that for the most part, there is rarely anything tangible to observe, measure, or experiment on, is there. (Of course you have the CERN collider which aims to add this element of observe, measure, and experiment to the theoretical work, but most of the time observing, measuring, and experimenting is impractical. And noting their work rarely begins from observation either).
So for the most part, 99.9% of the time, what theoretical physicists do is leaps of logic and guesswork. They put these leaps into the language of mathematics and see do those leaps make sense in the exact language odf mathematics.
Actually what all science consists of is a series of best guesses, at heart. You then draw on logic and mathematics and so on to develop a theory that supports your best conjecture (as an experienced scientist, in other words, we are typically talking about educated guesses).
And when you have the theory satisfactory, when it stands up to peer criticism perhaps, then you try and go out and test it in the real world to try and find a case that disproves it (not proves it).
For example when Einstein made his leaps of logic and guesses to work out his general theory of relativity in mathematics, he then went and sought out some phenomenon that might disprove his theory. He was lucky in being able to get Arthur Eddington on an expedition to Africa to observe an eclipse of the sun, to observe starlight passing close to the sun to see if it was deflected in agreement with his idea. Einstein said, "If the redshift of spectral lines due to the gravitational potential should not exist, then the general theory of relativity will be untenable."
But much of his time, as a scientist, was spent in leaps of logic and best guesses.
Anyway, people guffaw for various reasons at the true statement that science consists of "... leaps of logic, it's guesswork...". That's because they don't understand what the man is saying - they don't know what this scientist knows, they know only what they themselves know, and they judge his statement on that basis, on their own ignorance.
This is a terribly common affliction in the internet age.
