Isn't red usually associated to danger or to something you want to avoid as opposed to green?
This would be a cultural interpretation of the color red. In China, it represents good luck and happiness (Wikipedia). You can see more about what different colors generally represent in different cultures in this Information is Beautiful Infograph: Colours in Cultures.
To look at your two specific examples:
Rotten Tomatoes uses two distinct ratings of "fresh" and "rotten", with a "fresh" movie having a rating over a certain threshold (60%, I think) and anything less being "rotten". As such, these two ratings are associated with a nice plump red tomato or a glop of green goo. They have matches their meter colors as a result.
The Verge uses a scale of scores that is color coded, it is listed on each review page towards the bottom:
You can see that is runs the visible color spectrum with 10 being a "warm" red, and 1 being a "cold" blue. As a result green is lower on the scale.
Here is another article on the color red, from Designmodo: Evoke an Emotional Response: Using Red as a Design Tool. Note that while "danger" is a consideration, it is not universal!
In the end, is the use of red in these rating systems significant enough to produce an emotional response in the user that is contrary to what the designers intended? That is only something that user-testing can really tell you; and given the use of the color and the greater audience I would assume it doesn't.