I have been looking at the formula for propagation of uncertainty in physics, but I thought my question was better suited for maths stack exchange.
I have been thinking about it in terms of Phythagoras' theorem, and since the variables $X, Y,\ldots$ in this formula are independent, they have orthogonal directions. So in terms of Pythagoras' theorem, I would think that the formula should be
$$(\Delta R)^2 = (\Delta X)^2+(\Delta Y)^2 + \cdots$$
I really don't understand where the partial derivatives come from.
I have looked at the multivariable chain rule as I read that this formula was based on the multivariable chain rule, however I don't see the link!
EDIT ADDED AFTER READING THE ANSWERS
25/12/2016
So it seems to me that my confusion lies in the fact that the variation of $R$ in the orthogonal $x$ and $y$ directions is not just $\delta x$ and $\delta y$ and the orthogonality is needed to use Phythagoras' theorem. I'm not sure if this is a correct way of thinking about this, but perhaps this has to do with the orthogonal 'axes' for this being skewed or not exactly orthogonal in a certesian coordinate system, which is why the partial derivatives are needed to decompose R onto these orthogonal axes?
I don't think I'm making much sense, but in a nutshell, could linear algebra and basis sets provide an answer to my question? If so, does anyone know what topics specifically it would be useful to look up/Google search to understand this better?
Could someone please tell me where my 'intuition' has gone wrong?

Your intuition is right but you have to replace $\Delta X$ with the error along $x$-axis of $R(X,Y,\ldots)$, $\Delta Y$ with the error along the y-axis of $R(X,Y,\ldots)$ and so on...hence it would be better to write:
$$\delta R=\sqrt{(\delta R_X)^2+(\delta R_Y)^2+\cdots}$$
where $$\delta R_X\approx{\partial R\over\partial X}\delta X$$ $$\delta R_Y\approx{\partial R\over\partial Y}\delta Y$$ are the first order variation of the function $R(X,Y,\ldots)$ along $X$ and $Y$ axes respectively.