I'm sorry you're having trouble viewing your .htaccess files through CuteFTP. I tested this by downloading a trial copy of CuteFTP. I was able to view .htaccess files with our without server side filtering enabled. Just to be clear are you enabling server side filtering as shown in the screen shot below:
You can also view files in your account by using the cPanel File Manager. Just be sure to select the box beside Show Hidden Files.
If the issue persists, please feel free to either update your question or add a comment below with step-by-step instructions to replicate the issue (including your FTP settings in CuteFTP).
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