He makes cooking seem simple and fun.
Means that when he cooks it looks effortless and enjoyable. This is usually meant to indicate that someone is very proficient and things that are complex and thus cause annoyance to a normal person are routine and easy for him.
An example would be a chef who does one of those fast chopping routines of vegetables when you watch a professional do it, you feel as though it is easy. When you go ahead and try though usually you figure out that the knife sticks, the vegetable isn't cut through and slips from your grip and you cut yourself.
He makes cooking simple and fun.
Means that he actually shows/teaches/helps you in such a way that the cooking really ends up being simple and fun.
An example could be someone who teaches easy but delicious recipes that it is easy to cook but they look fancy or it might be a friend who cooks with you and through skill helps you in such a way that the stuff you end up doing is fun.