The fix to make .htaccess files visible is quite simple, you have to modify the file browser view filter to show hidden files but hide certain file types so you won't get a mess in your view.

First goto the filters menu by clicking the little arrow on the top right of the file browser and click 'Filters...'.

See the menu below:

When you are at the filter menu you will see the following window:

In this window uncheck '.* resources' and check 'Name filter patterns (matching names will be hidden):'.

Now you have to add a filter because you will be flooded by hidden files in your file explorer.
The filter I used is:

._*, .svn, .cvsignore, _notes, .*.swp, .DS_Store, .AppleDouble, .project, .buildpath, .settings, .git, .nbproject

You might append more filters to your needs.

In case you have a remote filesystem plugin installed you might need to check 'Show hidden files' in your preferences.

This is an example how this window might look:

Another handy thing to know, never edit the .project file!

That was about it for now, happy coding!