As long as papyrus was still easily available, the roll was indeed cheaper to make, since it required much less skill to create--the bindings of codices are complicated, easy to foul up, and required expensive additional materials (like glues and bindings) in greater quantities. Some sources will cite the scroll roll as being more expensive than a codex. It really depends on the time, the place, and materials. In the aggregate of all that, codices tended to be more expensive (and more and more expensive as time went on). During the high empire, the differences in cost were probably fairly negligible.

Once the papyrus sources were mostly cut off, mechanical considerations were added to the fact that codices were superior in many other ways (as you mentioned). Parchment and vellum, being more durable than papyrus, is much better suited to a codex than a roll: it can withstand bending better, and can survive the binding to the spine better. This is not to say that there were not papyrus codices, as some very early examples exist (from Oxyrhynchus, e.g.).

Some scrolls stayed around for conservative reasons, particularly in the Imperial government. There was no real reason to switch, and scrolls were just fine and had been working for centuries. When you have a gaggle of Imperial household slaves to assist you with storing, handling, and reading papyrus scrolls, there is little incentive to do something different. Some suspect that codices grew in popularity because they were much better objects for non-elite, who didn't have large spaces to store and read cumbersome scrolls. Christians seem to have played an important role in the adoption and transmission of codices. Use of scrolls persisted in some functions simply due to tradition and the airs one could put on--so for instance, with official decrees, which needed to have all the weighty seriousness of the stern Romans of the Old Republic.

It is often noted that codices are much easier to transport than scrolls, since they stack and are not easily crushed, unlike a stack of scrolls. They are also generally better at protecting the paper contents, and as vellum and parchment were very expensive, it made sense to package it and store it a way that offered more durability.

It's a great topic and, as you can see, there are no really clear-cut answers. As usual, the real answer is "well, it's complicated." There are some great books out there about the humble history of the book. One that commonly appears in the University classroom is Clemens and Graham, Introduction to Manuscripts. (Cornell 2007). There is also an entry in the "Companion to" series, which has excellent basic chapters on a plethora of subtopics in the history of the book. Great publication. It is Eliot and Rose Companion to the History of the Book (Wiley-Blackwell 2009).