good, cheap lunch in Malibu
In my opinion, a better alternative to Neptune's Net is Malibu Seafood on the PCH, a little over a mile north of Pepperdine. Grilled Calamari sandwich is always well made and tasty. Eat outside and overlook the ocean and beach. Laid back, good prices, good food. Whatever you do, have fun.
I don't know what you consider cheap, but malibu Kitchen has some very good stuff (sandwiches, deli case, baked goods). Also in the country mart is Tra di Noi (across the street, past the playground) has a takeout window in addition to sitdown dining (there's public seating in that courtyard) and good sandwiches (steak sandwich is very good), pretty tasty pizza, etc. In that same courtyard there's place that's supposed to have pretty good burgers, but I forget the name (Howdy's, maybe?) -- but I've never been there myself. There's also a Marmalade Cafe near Malibu Kitchen -- it's a small chain, and while I've never been there, I think it's supposed to be good.
Much further up the road (north end of Malibu -- 20 miles or so) is Neptune's Net. Not the greatest (or healthiest) fare -- lots of fried seafood, stuff like that -- but kind of a fun place to go, popular with bikers.