How can I rotate a pdf document using php and linux?
You could use pdf90 from PDFjam.
To address some of the other suggestions:
I would be wary of adjusting the Rotate attribute directly, as this attribute is stored as text, and '90' or '270' obviously uses a different number of bytes to '0'. I believe inserting the required bytes can make a mess of the index tables that appear at the end of a PDF file. After that, you're reliant on a viewer being able to interpret the damaged file.
Rendering the PDF to an image and rotating that is going to rasterize any text or vector graphics, leading to either a much larger file size, or much lower quality.