If those log files are still in the directory you’re trying to delete, you need to get rid of those first before you worry about whether you have .htaccess files lying around.
Are you running PHP as a CGI or under Apache? This is a checkbox option in your Domain HTTP details. I’m guessing that your problem is that you have PHP running under Apache (the non-recommended option…), so those log files belong to the Apache user instead of your user.
If you know how, you can write a short PHP script that will delete the files (don’t change the CGI option until after you’ve done this) – if you don’t know how to do this, ask support to help you out deleting those files. And before you install again, change that “run PHP as CGI” setting.
Finally, you definitely need a standard FTP client. Something like FileZilla would work fine, and would make it much easier for you to see which user owns those files you can’t delete, the hidden files, etc… Plus then you can use SFTP (Secure FTP) so that your password isn’t going over the network in plain text where anyone can grab it. Yes, it’s nice to be able use an FTP folder as is if were just any old folder on your PC… but as soon as anything goes wrong, you’ll have a much easier time using a tool that actually understands that you’re accessing files on a Linux server.