If you have your sites hosted with Bluehost (affiliate link) you have a tool called the Index Manager that can handle this problem for you.

The Index Manager allows you to customize the way a directory will be viewed on the web. You can select between a default style, no indexes, or two types of indexing. If you do not wish for people to be able to see the files in your directory, choose no indexing.

• Log into your Bluehost control panel.
• Locate the Advanced menu.
  

  Bluehost Advanced Menu Panel

• Locate and click on the “Index Manager” icon (third icon from left).
• This will bring up the Directory Selection box.
  

  Directory Selection Box

• Choose either the Web Root (public_html) or the Document Root. If you have multiple domains select the domain you want to index from the drop down box.If you do have multiple domain names please be careful not to check the “Skip this question, and always open this directory in the future when opening.”
• This will bring you to the “Index Manager Menu” that will allow you to navigate to different directories.
• You can navigate to different directories by clicking on the folder icons. Select the directory you wish to index click on the directory name and your “Index Manager” will offer you  four options: a default style, no indexes, or two types of indexing. If you do not wish for people to be able to see the files in your directory, choose no indexing.
  

  Index Manager Options

• Make  your selection then click the “Save” button in the center of your screen. You will then receive a confirmation page showing the updated settings.

Now if someone clicks on a folder that does not contain an index.htm file, they will receive an error message like
Forbidden
You don’t have permission to access /images/ on this server.

You can also customize the page and message your viewer receives by customizing the 403.shtml file.

Very simple to do and no one will see a listing of your files again.

I use Expression Web as my web editor and publish using the ftp facility from within the program in most cases. I had been using Filezilla to publish to the main domain frontpage-to-expression.com as there are two of us who maintain the site. Imagine my surprise the first time I used the ftp client from within Expression Web to have the program compare the domain I was publishing to ALL the folders for every domain within the public_html directory. Read the full tutorial