Why are ecology and economics seemingly disjunct topics? The words ecology and economy are very similar.  Ecology derives from the words οἶκος + λογία, i.e. the study of the house/household.  Economy derives from the words οἶκος + νόμος, i.e. the laws of the house/household.  In modern usage, ecology studies, among other things, movement of materials and energy through living communities (e.g. Wikipedia).  Economy, in modern usage, is defined by Wikipedia as An economy or economic system consists of the production, distribution or trade, and consumption of limited goods and services by different agents in a given geographical location.
An interdisciplinary field is called ecological economics, which is the treatment of the economy as a subsystem of the ecosystem (again according to Wikipedia).

I've often wondered by ecologists and economists seem, often quite literally and physically, separated fields.  Ecological economics considers the economy as a subsystem of the ecosystem.  Why is this not standard?  How can the economy ever not be a subsystem of the ecology, and why is not all economics "ecological economics"?  Or is it?
I think you are right to say that an economy is always a subsystem of a larger ecosystem, but it needs not always be modeled as such.

It may be interesting to have a precise and elaborate model of the solar system taken in isolation, independently of its interactions with the rest of the galaxy, other galaxies, etc. In very much the same way, there are many good reasons to build a model of an economic system without accounting for how it fits in a more general ecosystem. 

The same kind of question applies to many other topics. One could for instance ask "why partial equilibrium and not always general equilibrium?", "why small open economies instead of replicating the actual size structure of the global economy?", etc. I guess the only answer is that the smaller, less general models are considered useful in one way or another.

This is not to say that the opposite endeavours (the ecological economics attempts to model economic systems as part of an ecosystem) are worthless, quite the contrary. But there is only so much you can do and there is always a trade-off (in terms of estimability, tractability, additional assumptions, you name it ) to increasing the generality of a model.