small note from the biochemist, proteins can be hormones. However ephedrine, aka adrenaline, is not a protein.
As to the question, while it has been linked to those markers, an actual effect has not really been seen. There is no major link to coronary heart disease, which would be expected in the coffee was causing major inflammation. Also, coffee has been linked to beneficial effects when taken in moderation (less then 4 cups per day, which is still quite a bit), and this is looking at overall systemic effects, which means that if there was an increased risk of problems linked to the inflammation markers, it would have been seen.
However, this was also, if memory serves, an epidemiological study, and so confounding factors are rife. However, there still is little to no evidence to suggest any major harmful effects as long as the coffee consumption is not excessive.