That is an apples to oranges comparison. Hence the terminology difference between transpiler/compiler.
A transpiler is a very specific subset of a compiler that takes one language that has a "similar" level of abstraction and compiles it to a different language with a "similar" level of abstraction.
C++ compiled to machine code is not at all similar to CoffeeScript transpiled to JavaScript.
If you are working in CoffeeScript/TypeScript/Opal you are still likely to need to understand JavaScript to best leverage existing JavaScript libs/frameworks and to build on or debug those tools when necessary.
A couple of problems arise when you introduce something like CoffeeScript. Now you have added yet an extra layer of knowledge required to the infinite pool of required knowledge
Problems
1) Knowledge required
Now your team is required to know
CoffeeScript(Replace with other transpiled language here) + JavaScript + HTML + CSS + Backend Language of Choice
2) Hiring pool
Eventually you will need to hire someone. This presents a problem from both the employer and employee side
Employer Side (Pointy Haired Boss)
We use CoffeeScript/TypeScript/etc... so we need to post that as a job requirement.
Employee Side
Really smart potential employee who wants to apply knows JavaScript; sees posting requires CoffeeScript. This employee hits indeed.com and sees there are <1000 coffeescript jobs total, versus >43,000 javascript jobs. Employee decides to stick with JavaScript and doesn't apply.
This is a bit of an old interview and I don't know Jeremy Ashkenas personally so I don't know his current stance of CoffeeScript, but I'm going to post it here since it's from the horse's mouth and I believe it illustrates why using JavaScript is really a better choice.
"If the question is 'why is CoffeeScript not a DocumentCloud project?' - it's because I can't justify using it for the main DocumentCloud development. Imagine trying to hire someone. 'You'll have to learn to use a new language that we made up...'" - Jeremy Ashkenas
http://readwrite.com/2011/01/07/interview-coffeescript-jerem...
3) Future proofing
I'm just going to link back to the same wycats link someone else posted, because it's much more elegant than how I'd put it.
https://meta.discourse.org/t/is-it-better-for-discourse-to-u...