WordPress install hacked

My WordPress install was hacked, after a couple of days of trying to find the source and searching the internet I found out it was this http://blog.sucuri.net/2014/05/website-infections-malicious-redirect-to-porn-website-target-wordpress-and-joomla-users.html

I then check all my index.php files and they all showed normlly, however the index.php in the wp-content folder when I copied and pasted the content revealed somthing else.

It was origionally

<?php// Silence is golden.?>

When I copied and pasted the content from notepad++ to google as I wanted the check the silence is golden is normal I noticed it changed into somthing else entierly :

[ Massive amount of obfuscated hacked code deleted, you don’t have to share that part ]

Firstly no other files behaved this way when I copied and pasted them, I am far from an expert but if some one could let me know a couple of thing:

1. Why couldn’t I see that when I was looking at in via ftp using notepad++, why did I have to copy and paste it to see it.

2. Is that the likely cause of my the websites redirecting when viewing on mobile?

Thanks for your help in advance.