There are a few programs that will try, but as dave says its messy. You loose a bunch of formatting, paragraphs get screwy, images and tables get borked. 
What I do is actually read PDFs in Adobe Acrobat for iPad (I tried avoiding it for months, but found it works best - simple, easy, reliable). You can double tap and it zooms to fit the main paragraph. I was using iRead since it had a neat feature that would lock horizontal scrolling of PDF's when zoomed (acrobat doesnt), but it was constantly crashing on me. 
Oh and the key feature for me is continuous scrolling. No page turning, no snapping. I also used Goodreader for a while, but you have to pull to the end of a page, release, then pull again to get to the next page. iRead and Acrobat will just keep scrolling all the way through. 
Try iRead first, zoom in, then lock horizontal scrolling so it stays focused on your content. Maybe it wont crash as much for you.