What that means is that it doesn't matter if you're measuring in pixels, or inches, or kilometers. It's more important that everything in your model (or really, in a 2D drawing) is appropriately sized in proportion to the other objects in your scene. You wouldn't model an elephant the same size as a house, unless you're animating a short called The Attack Of The Mutant Elephant. If you're modeling a one-story house, say a cottage, the elephant might be about half to two thirds the height of the cottage. Many times you'll end up eyeballing your measurements this way.
A lot of 3D animation programs will allow you to define units of measurement that you can use for reference. A 50-pixel area of the screen may be defined as a foot in the 3D space, so that you have a ruler to use for reference in accurate modeling. This is especially useful when recreating things accurately, perhaps if you're creating a scale modeled replica of the Empire State Building or creating characters who have specific heights in reference to each other.
Think of it in terms of a map. Maps come with a scale that tell you how much distance equates a mile or a kilometer, so that you can estimate the distance between one point and the next. Units of scale in 3D modeling just upgrades that a little, and gives you the freedom to define your scale. Another way to think of it is as a scale model or a diorama; when you're putting together a scale model of a scene, building, or other landmark, every object in the model has to be perfectly in proportion to the original, but on minuscule scale.
While many people guesstimate their scale measurements when modeling or drawing, this takes a lot of practice and observation. When you're first starting off, you'll want to create some kind of unit of measurement for scale, or use one already built into your program. I confess I've been known to hold a piece of paper up to the screen and mark off units on it for comparison, to make sure everything is scaled properly.
Work out whatever method fits your animation style and workflow best. Otherwise you may end up creating objects that are just far off enough in size to be jarring and ruin your animation, rather than fitting together seamlessly. It can be especially difficult to guess when you're working with perspectives in a 2D or 2.5D space.