Why? At first, the cost seems like a ripoff; publishers don't have to pay for paper, ink, or postage, so you'd think the content should actually be cheaper. Then you calculate in the cost of interactive designs and features, researching new technologies, and creating new workflows, and creating an iPad version of the magazine starts to get more expensive. Throw in that publishers are wary of pricing their content too low, and you get a higher price than a print subscription -- which plenty of readers will probably pay anyway.
That's a pretty fragile pricing state, though; e-books are already cheaper than their print versions, and while comic books are the same price in the store as they are on something like the Marvel application, you have to think that those prices will drop too. As usual, early adopters will pay the most, but I wouldn't be surprised to see the price of "e-magazines" drop as publishers and consumers alike even out the rough edges of the transaction.