I would think it's due to a lack of representation (although I think I've seen some remedy towards this, still isn't enough to make much difference though) and just that Ike has a lot of trouble with top/high tier characters; I'm looking at King D3, LOLimar, and Flaco. Feel free to add MK if you want to, even though almost everybody has trouble with him anyway so bleh. There are probably other characters too, but I can't tell you anymore due to me not keeping up with his metagame (though I'm sure not a lot has changed, sadly..).
There's that, and just how he feels slow, sluggish, very punishable, and is closer to the bottom end of the spectrum of characters who can recover.
Lowest I'd put him would be at the mid-point of low-tier. Inui may be coming in here and telling you he's the 5th worst character, but I'd put Samus/Lucas/other characters there before I could begin to consider Ike THAT bad.