Well, using capitalism to explain other issues is just a consequence of being a Materialist.
If you adhere to a materialist understanding of the world, you come to the the conclusion that most of the features of our environment (which is validated by analysis) find their roots in the material organization of our world. And the material organization we are operating in is "capitalism". Which is why it applies so much.
I think part of the confusion comes with the understanding of what capitalism is. Capitalism isn't markets, we had markets before capitalism. Capitalism is the economic organization where:
* Production is organized under private ownership
* Social relations are dominantly monetary relationships
* Labour is dominantly done for wages
* Production is done for profit
* A market system is used to structure productive relationships
* A de-facto class system which divides workers and owners
That's what capitalism is, and when people, especially academics say that something is caused by capitalism, they refer to capitalism as defined, loosely, by those elements. Capitalism is not a tool, it is a state of being. Markets are a tool, that have wonderful advantages. Markets aren't an ideology, capitalism is a group of ideologies that promote markets as much as possible. For an extreme example, in the USSR, food production was overwhelmingly mediated by markets. Was that capitalism? No, because it was not done for profits, and because production was not based on wages.
Everyone agrees that markets is an amazingly useful tool and is fit for many applications, except some which lack a good grasp of economics, or others which are deluded into abstracting economics from society and which therefore miss when they are not fit for the task. What people don't agree with is that capitalism is a system which should be perpetuated, and the two are perfectly consistent positions to hold.