I have experienced this and fixed it. Here is how I did it. I went in to my FTP to change my .htaccess file permissions from read-only to writable. Then, I made the changes I needed to so that W3 Total Cache would work, then I returned my .htaccess file to read-only permissions.
1. Log in to your website via FTP (I use FileZilla, but you can use any other FTP client or use an FTP file manager like what GoDaddy offers, you can probably access your site files in your FTP in cPanel as well).
2. Edit permissions of your .htaccess file. I'm using the Bulletproof Security plugin, so that automatically prevents any and all changes to my .htaccess file. Some other plugin is likely doing that for you too. My permissions were set to 404 (read-only, you can use 0404 if your FTP client requires four digits), I had to edit them so that my .htaccess file is writable. I set the permissions to 705 (0705). Not sure how you do this with Windows hosting (which isn't that great for WordPress anyway, you may want to consider switching to Linux hosting if you aren't already on it), but you can make your .htaccess file, and all other files and folders, writable with Windows hosting.
3. Once I made my .htaccess file writable, I just copied and pasted the changes that W3 Total Cache wanted to make into the top of the .htaccess file. (For Bulletproof Security, I had to go to edit functions.php to turn off the annoying BPS security warning that shows up in my WordPress dashboard. Google it for more info if you're using BPS. If you aren't using BPS, don't worry about this part in parentheses.)
4. Optional, return your .htaccess file to read-only permissions (404 or 0404). If you use lots of plugins that edit your .htaccess file, you'll either have to leave your permissions at 705, or you'll have to do this manual editing process every time you change your .htaccess file. Changing your .htaccess file to read-only mode is better from a website security standpoint, but it's more hassle to change around. Leaving it writable is a little less secure, but is more convenient to make changes.