I understand the formulae for combinations and permutations and that for the binomial distribution. However, I'm confused about their application to coin tossing.
Consider three tosses. Outcomes with two heads are HHT, HTH and THH. So, there are three and that's what you get if you use the formula for combinations.
With combinations "the order is not important". How does that apply in this case? In what way are these three outcomes different if the order is not important?
What are the 6 permutations?
Imagine that you have three balls numbered $1$, $2$, $3$ representing the flips on which heads may come up. (I'm using your scenario of three flips). You want to look at cases where you get two heads in three flips, so you are going to pick two of the balls. Picking first ball $1$ and then ball $3$ gives the same result (sequence of tosses) as first picking ball $3$ and then ball $1$ (both result in the outcome HTH).
Thus you are making an unordered selection of two of the three positions.