Nadal Has History of abuses
Another reason for the angry reaction to Nadal's medical time-out is his history of abusing the system.
Here are examples from memory that I've watched:
1) Hamburg final.06, I think. Federer is about to serve for the set. It's not a change-over. Nadal suddenly takes a 6 minute time out (beyond code) to have his thigh massaged. {Seriously, a 6 minute thigh massage.} As the European announcers noted, Nadal showed no sign of injury before or after during that match, nor did he have problems in a subsequent tournament. It worked. Fed had been dominating, but came out cold and blew the set.
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2) Monte Carlo. Again, Fed is serving for the set and Nadal takes a mystery time out. Works again.
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3) Vs. Murray, can't recall the venue, but Nadal does the same thing when trailing. Amusingly, a month later, perhaps in Cincinatti, Murray asked for a medical timeout before his opponent serves and the chair tells him that isn't allowed. Murray says, "Nadal does it to me." The chair (Mohammed Leahni) just throws up his hands?
This, of course, comes on top of Nadal's incessant time violations on serves, refusal to come out and start matches on time, his admission to being regularly coached from the stands, and gimmicks like holding up his hand at the last minute to stop servers when he's trailing.
I suspect this comes from his family's soccer back-ground where diving and tripping are considered OK if you get away with it.