I'm trying to copy a text doc to a web server and no matter what I try I am getting "not a regular file"

I have tried probably 20 different combos of source & destination locations, changed file name, changed file permissions & even tried different files. I have tried a plain text fil and a script with a .pl extension. the thing is I can copy any of them with WinSCP...

I have tried
User@Computer:~$ scp username@domain.com:/the/path/to/my/folder/ ./transfile.txt
User@Computer:~$ scp username@domain.com:/the/path/to/my/folder/ transfile.txt
The above I was always in the folder with the file. I haver added the full file address as well. I have tried as root and as a super user command. Nothing works for some reason, but my windows machine with WinSCP will send it (hosted from the linux machine that won't send the file, so it isn't a different file)

Any ideas how to fix this or what it might be? I'be had this happen before but had to move on to other things. BTW I'm running Ubuntu 14.04

You are using the command improperly.
The command as you provided it (NOT enclosed in code tags, as it should be) does attempt to copy the folder on server into the file and scp is (quite properly) telling you it cannot do that because you cannot copy a folder to a file.

Did you read the man page on scp?

I suspect it is because you have mixed up your source and destination in the command. Could you tell me if that may be correct?

The syntax for scp is just like with mv, cp, rsync, etc.

If you want to copy transfile.txt to domain.com, then you have the source and destination backwards. As wpeckham said, the error is because your command, as written, is trying to copy a directory into a file, which is nonsense.