We build *static* structures that are larger. The aircraft carrier floating on water means that no point of the structure has to bear much of the weight - load bearing is evenly distributed across the entire surface.. Also, it is mostly hollow (which is how it floats) so the aircraft carrier is surprisingly *light* for its size. Both of these things are build with few to no real moving parts, and a great deal of thought put into distributing the weight evenly across the entire footprint of the object. Large buildings are not built to do the Hokey Pokey. Contrast this with a typical, bipedal kaiju (say, Godzilla). It walks. It can do the samba, and moves seen only in pro wrestling. It has joints at ankle, knee, and hip. As it walks, legs alternate bearing the entire weight of the beast - so those joints have to take shifting loads generated by the entire beast, rather than distributing them around like we do with a skyscraper or ship.
Here's the science. The strength of a piece of material typically rises linearly with it's cross-sectional area. So, it rises like the square of a typical dimension of the piece. However, the weight of the object rises linearly with the volume of the object, so it rises like the *cube* of a typical dimension of the piece. So, you have material strengths going like r^2, but the loads going like r^3. This means that for any given material, there's a point of size beyond which it cannot support its own weight, and it will collapse. And this is without considering dynamic loads on parts of a moving object, which can be several times greater than the thing's weight.
Yep. But we thought they were impossible on biological grounds, not on physical ones.
Which is what I've already said, several times over - if we have kaiju, we have materials we don't know about, with properties we cannot reasonably predict. Bunker-busters are built to penetrate good old fashioned reinforced concrete and armor plate. These materials are balsa wood by comparison to what keeps a kaiju walking. Ergo, we cannot clearly say that the bunker-buster is going to do a whole heck of a lot.