Apart from the ability to resize in IE6 (which is still, alas, a very popular browser), relative fonts give you a greater likelihood of matching the user's needs by default without them having to resize (or knowing how to, if we're talking inexperienced users here). The user — or someone on their behalf — may have increased font size as a DPI, OS or browser customisation for good reasons (eg. visual impairment) and with relative sizing you can use that information to their advantage.
Use ‘px’ for text that has to match sizes with other on-page elements that are sized in pixels (ie. images). For the rest, ‘%’. The question assumes that using relative font sizes is in some way difficult; I don't think it is.
Typically you'll set one font-size in ‘%’ on the body, and a few on other page elements which are more or less important than general body text. You should rarely have enough levels of nesting and nested font-sizes that you can't easily keep track of them.
There is not anything about sizes being relative to their parent's size that is particularly hard to understand, and this property can be useful: should you want to change the basic font size on your page or a part of it, you can just change it once rather than having to go through fixing up every font-size declaration on contained elements.
The only real difficulty with relative is when you've sized a block relatively, but you want to size something inside it back to the original size. You can work out a percentage that's the inverse of the parent's percentage, but it's likely to be an ugly number, and you may get 1px rounding errors if you don't/can't state it in full accuracy. In this occasional case it may be a good idea to step back and look at the selector, see if you can't apply the sizing more selectively to avoid having to undo it.
It would, admittedly, be nice if we had a unit that was relative only to the user's default size, not parent sizes, to attack problems like this. Unfortunately the only values that work like that are the smallest/smaller/small/medium/etc. keywords, which are rather coarse-grained in addition to the historical browser consistency problems.