Having literally just flown TAM from New York to Sao Paulo (and connecting within Brazil), my experience was somewhat different than the author's.
All of my six flights left no more than 15 minutes after scheduling and all arrived on time, as did all of our luggage. The lines were no different than any other international flight.
In New York, TAM was kind enough to accomodate my belated request that my party of four sit in the same row (though our tickets were seperately booked and the plane was almost full). In Sao Paulo, TAM's gate workers were kind enough to notice that we were traveling with a baby and bumped us to the front of the connecting line (a common practice in Brazil, as with the eldery and infirm), a practice which was repeated for the return legs. TAM's flight attendants were even kind enough to remind passengers that reclining all the way back while the person behind was trying to eat was rude (though the legroom was small already).
If TAM had problems, they were not evident to me. Brazil has problems, however, most notably that one must fly through Sao Paulo (no, not the airport involved in the crash) to get anywhere else in Brazil and that U.S. citizens need a visa. But those are actually George W. Bush's fault, as Brazil has enacted these measures in retaliation for Bush's treatment of Brazilians. Neither situation applied during Clinton's term. And Brazil's internal labor and traffic control problems are well documented, neither of which affected my flights.
The author had a bad experience. They happen. But its not clear if she is merely ranting or if she actually has her facts in order. If its the former, the article is a horrific example of journalism.