This is very common in the military and in defense contractors, and it happens elsewhere too. There is a reason for it. Many of these organizations are worried about malicious stuff going in and/or exfiltration of non-public data going out. Employer MITM makes it easy to examine every packet for these kinds of things (to counter them). In the US, at least, it's generally accepted that employer equipment is owned by the employer, and thus they expressly have the authority to examine what goes over their own network... and as a condition of employment or computer use you probably signed something agreeing to this. I'm not a fan of this approach, but it certainly happens.
Open source software that implements crypto protocols (e.g., SSL or SSH) will (correctly!) report that there's a MITM attack. So if you want to actually *use* the software in such settings, someone has to configure the software to trust the MITM. Some admins will do this automatically. If not, you may need to do it yourself. E.G., on Firefox, install the organization's certificate.
You configure Linux systems to work in these environments, but since the certs are often files in Windows aka DOS aka CP/M format, you need to convert the files as well as put the into somewhere useful. Here's one way to deal with it.
On Fedora, given a bunch of .crt files, you can do this:
dos2unix *.crt ; cat *.crt >> /etc/pki/tls/certs/ca-bundle.crt
On Ubuntu, you can do this given a bunch of .cer files:
dos2unix *.cer ;
rename 's/.cer$/.crt/' *.cer ;
ca=/usr/share/ca-certificates ;
mkdir -p $ca/MYORG ;
cp *.crt $ca/MYORG ;
cd $ca ;
ls MYORG/* >> /etc/ca-certificates.conf ;
update-ca-certificates
You could avoid appending to the file if you want to, but I'll leave that as an exercise for the reader.