Thibaut Courtois is one of the best goalkeepers in Real Madrid's history and he has spent many years proving it between the posts. Florentino Pérez is aware of his goalkeeper's level and this is the reason why he has kept him despite his serious injury. Upon returning, the Belgian has shown that his level remains very high and that there's no one who can replace him.
Real Madrid is going through a restructuring process and they're closing major signings with the intention of turning the situation around. This season, Los Merengues haven't achieved the desired results and several members of the squad have lost credibility. However, it's become clear that this isn't the case for Thibaut Courtois. Florentino Pérez wants to reward him for it.

Florentino Pérez's management
Florentino Pérez is, without a doubt, one of the best presidents in Real Madrid's history and in European soccer in general. The Spaniard has spent years in the presidency and his management has been truly beneficial for the club and its fans. He has always put the institution above everything else and has done everything possible to take Real Madrid to the top.
Real Madrid is used to winning absolutely everything and this year has made Los Merengues suffer more than usual. Thibaut Courtois is one of the longest-serving members of Los Merengues and his loyalty is unquestionable. Despite having received very tempting offers, the goalkeeper has always put his team first.
Florentino Pérez is aware that Thibaut Courtois has done everything in his power to stay at Real Madrid and return perfectly from his injury. The president wants to reward him and will increase his salary over the next two years. This goes against Florentino's policy, since he never improves the salary of footballers who are over 30 years old.
Thibaut Courtois, Real Madrid's hero
Thibaut Courtois is one of the most beloved members of the squad and all the fans pray that he'll stay as long as possible. In the worst situations, the goalkeeper has stepped up and given his team victories. Florentino Pérez will reward him and will benefit his protector financially.
Thibaut Courtois has a lot of soccer in his boots (and in his hands) and he'll keep showing it at Real Madrid. Although we can't take anything for granted, it's likely that this salary increase will be announced soon.