You can configure buttons to appear at the bottom of the screen in the atomic browser. It's nit just recommended for that though as it has tabbed browsing and an ad blocker. Well worth the money for the paid for version.
That annoys me too, you would think with all the consistency garbage involving the mute switch they would match up the menu bars on the applications. But frankly I think the ipad has it right being on the top.
Also I wish you could make the bars disappear to gain that extra half inch, does atomic do that? If so I may just look into it.