I tried to copy and paste the features list in the ProTube cydia description but it won't let me. Them I tried to find that list online but I was unsuccessful. Your best bet is to just look them both up in cydia and read each package's features list. If you only want to convert the files to mp3 then youtubetomp3 will be fine. But ProTube allows that or you can download the actual video. it removes and blocks almost all advertisements. You can choose what resolution you want the video to play, 1080p, 720p, etc.
If alls you need is to download the file to mp3 then YouTubetomp3 is perfect. Plus it's free too! ProTube costs $1.99 I think but I use it almost everyday and highly recommend it. Plus if you own an iPad, you get a free copy of the ipad version ProTube HD.
Good luck!
Edit: I made a mistake. The app is $1.50 not $1.99. And the other thing I wanted to point out was that you can also download another tweak to go with ProTube called "Open in ProTube" so whenever you click on a YouTube link, it'll open the video in ProTube instead of the limited stock YouTube app.