To expand on existing answer, like explained by ssl.com, a .cer file can be either in der or pem encoding. If it is in der encoding, you'll need to do conversion like you have done, but if it is already in pem encoding, no conversion is necessary and you get the error you've got if you try - and you can just rename the file.
If you're unsure, it is good to know that .der is a binary format, whereas .pem is ascii one. If you echo the contents of your certificate out, a .pem file would look something like this:
-----BEGIN CERTIFICATE-----
MIIEuTCCA6G[snip lots of chars]
XmCpajQ==
-----END CERTIFICATE-----
And a .der file would look like this:
0??0???@*?H?????0
0??1
0 UUS10U
VeriSign, Inc.10U
VeriSign Trust Network1:08U
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