A sample, as @CarVac said, would be helpful. Also, what version of the software you’re using and what platform you’re using it on (Linux, Mac, Windows).
Welcome and I hope you find this forum of use!
I’m comparing it to the raw photo, though it’s lighter than both.
I’m on 4.2.1375 and Windows 10. Working on a sample right now.
And this tools are marked with an 1:1 label in gui 
Remember the little raw preview shown in the browser before opening the photo is also a jpg generated by the camera internally and saved inside the raw. There are things you can do to emulate the look of the in-camera jpg’s. Someone recently posted an importable tone curve that mimics the camera process. Personal tone curve
No it’s not that, the raw photo looks fine when I open it within say Windows photo viewer. Only when I run it through Rawtherapee does it get all jacked up.
I don’t know about windows photoviewer but I imagine it is doing something to avoid displaying the image in linear gamma.
Windows Photo Viewer is viewing an embedded JPEG, which is identical to (but more compressed than) the separate JPEG.
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Also there is the default “auto-levels” behavior in rawtherapee which can be reset…
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Alright here’s a sample. Here’s the original raw image:
And here’s the same raw file run through Rawtherapee and exported as JPEG, no edits whatsoever:
Can you post a link to the actual .cr2? It looks normally noisy because I suspect auto-levels has raised the shadow areas more than you’re liking.
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You should be able to just drag and drop a .CR2 file into the post editor to upload it here.
Maybe you should start with this setting:
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Here: IMG_6660.CR2 (26.0 MB)
Okay so that has fixed the image being lighter than original, so that was an edit I made that somehow got saved, I suppose? Either way it’s still importing noisier than the original CR2.
With the neutural profile you are seeing the original raw. Opening a raw in rawtherapee has a default behavior of setting the contrast and exposure levels, etc. for you automagically.
Can I turn that off?
Okay so this is basically saying that the image I’m looking at in Rawtherapee is “more raw” than what I see in a photo viewer?
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I think you can turn it off. I leave it on its default behavior and click the reset button at the top of the exposure section, so as to not disable the other default behaviors. Nowhere near a computer so one of the others here or the rawpedia can help you do that.
You appear to not have read the link you were pointed to twice now…
See the “Processing profiles” section
http://rawpedia.rawtherapee.com/Main_Page