For fishing you want a sit on top. The sit in’s are too restrictive and have less storage. I’ve fished in both and I’d never own a sit in for fishing. I’m personally a fan of the Feel Free fishing yaks. Hobie will mostly be out of your proce range. Jackson has a few that start under 1k so used for 500 seems reasonable.
I've got a Heritage Featherlite sit-in that I bought before I got back into fishing, when my main criteria were low price and low weight.
It's served me well as a fishing kayak - they go for $599 new so used should be well under $500.
The cockpit is pretty open and I have no problem storing two rods, tackle box, and other assorted loose items like a scale, water bottle, etc.
http://www.heritagekayaks.com/hken/featherlite9-5.html
With a $500 budget go new for $550 at BassPro 10'
http://www.basspro.com/Ascend-FS10-SitIn-Angler-Kayak-Camo/product/14072306364312/
Light weight where you can pick it up with one hand and carry it, rod holders, plenty of storage, dry storage ... excellent seat which is one of the most important parts IMO. Only bad thing I can say is the hull isn't the thickest, don't drag it on the ground.
http://www.mafishfinder.com/view_photo_details.php?id=46729&pid=47
good luck