I think if people see rankings for what they are, there is no problem.
Rankings (in tennis, football or any other sport) DO NOT show which teams are definitively better than other teams. They are (or should be) the best possible approximation of the CURRENT strength of teams/players based on recent results. It is part of the fundamental essence of rankings that they will change, so a team can be 10 places higher one week, then drop 10 the next week - this does not show a flaw in the rankings, it shows that the rankings are adjusting to better represent the true current strength of that team. The importance is the word "current". Rankings are not supposed to be historical - this is the job of straight statistical league tables which would see Brazil, Argentina, England, Germany, Italy, etc. always at the top. And of course, as with everything else, there will be unexpected results.
A lot of people will say that, for example, a team who beats Brazil by defending for the whole game and winning 1-0, despite Brazil being clearly the better football team in the match, do not deserve ranking points. However, when you realise that the key purpose of football is to score goals, then it is clear that in this particular match, the winning team done the better job and was the strongest team in terms of achieving this purpose.
But, essentially, the more teams play teams from other parts of the world, the better a truly world ranking becomes, as there is more data. It is clear, for example, that the bottom teams in Oceania appear to be worse than the bottom teams from other continents. Even though American Samoa have never played Djibouti, it should be clear that teams who beat American Samoa 4-0 (Tonga, Samoa, etc.) are a lot weaker than teams who beat Djibouti 4-0 (Kenya, Tanzania, etc.) It is possible to show this in a decent ranking, and in my opinion, this is a good thing - it is a nice and neat way of showing this difference in strength. Without a ranking, it is not always possible to compare teams (hence why rankings are usually invented - people like to see where their team ranks). The winner of a knockout competition (such as the World Cup) does not necessarily deserve to be Number 1 - and only by having a balanced ranking can this be shown.