Because most magazine apps are still trying to look like print magazines they use static layouts. Changing he font size would mess up the entire page, so they don't offer it. There are a few exceptions, and at least one I remember that had an article reading mode that was pretty nice.
Since you are probably not going to buy a magazine based on it's bells and whistles (as opposed to content), you're stuck with the usual tools.
Besides switching between one and two page mode in landscape, most magazines support the pinch gesture just like Safari. By placing two fingers on the screen and moving the further apart or closer together you can zoom in and out of the text. Most magazines use farily narrow columns of text, so it is easy to fill the screen with one column and then scroll. While not quite as nice as increasing the font size, it doesn't take much practice before you're zooming around without thinking about it.
For any magazine that does not support the pinch gesture, there is still the iPad's Accessibility features; specifically the Zoom feature. While it is not a pretty as the pinch gesture it is not difficult to master the various gestures, and it works no matter what you are looking at.
You'll find it under Settings > Accessibility.