I don't think that this is true. It's just that C. Ronaldo and Messi spent the best part of their careers playing for La Liga teams. You can't really say that they didn't deserve it.
La Liga has "won" 23 Ballon d'Ors, but 10 of them are from Messi and C. Ronaldo. Serie A has 16 Ballon d'Ors. The Bundesliga has 9. If anything, I think the real issue is that the English top division doesn't get enough Ballon d'Ors! Just 6(one of them being Ronaldo) in total.
Since 1999, La Liga got 16 Ballon d'Or winners, EPL got 2 winners, Series A got 3 winners, PSG got 1 (though it was Messi), bundesliga got ZERO
Whereas La Liga won UCL 11 times, EPL won 6 times, Series A won 3 times, bundesliga won 3 times
La Liga is over-represented in terms of Ballon d'Or winners
In past 20 years, you only hear players from La Liga "robbing" the Ballon d"or from non-La Liga players, but never wise versa, and a lower standard is required for a player from La Liga to win the award than a non-La Liga player. You only need a worldie performance at La Liga alone to win Ballon d"or even if you do poorly in European and International tournaments, but if you only perform well in your English or German league, sorry, you are not qualified to win.
In 1999 Rivaldo won the Ballon d'Or for carrying Barcelona to top 4 in La Liga and his Copa America performance while Barcelona was knocked out of UCL in group stage.
In 2000, Luis Figo got the Ballon d'Or while he wasn't the best player for the year, but since he had that famous transfer saga from barca to Real Madrid
In 2005, Ronaldinho won the Ballon d'Or scoring 9 goals in La Liga with Barcelona getting knocked out in round of 16 (him scoring 4 goals), since Barcelona won the La Liga and Ronaldinho was the poster boy of Barca.
In 2010, Messi won the Ballon d'Or for his La Liga performance alone though he kinda stinked in World Cup 2010, and Sneijder who carried Inter and Netherlands to UCL title and World Cup final was ranked 4th, since Series A was not as sexy as La Liga and Netherland is not as sexy as Argentina, Brazil or Spain.
And the famous Lewandowski failing to win Ballon d'Or since he is a Polish playing in Bundesliga, which is not sexy enough.
Henry is undisputedly Ballon D'or winning level player but he never did so since he played in EPL in his prime which was not sexy enough.
It is also not only about Ballon D'or winners, Bundesliga and EPL players are much harder to climb up in Ballon Or ladder.
In 2011-12, Chelsea won the UCL, and van Persie had a worldie performance at Arsenal (and subsequently at Man Utd), but the Ballon D'or's top 6 are all occupied by La Liga players and van perise was only ranked 9th in Ballond'or.
In 2012-13, it was a German UCL final, no international football, but anyway, German clubs only earned 2 spots in Ballon D'or top 10, and La Liga got 5 spots. Gareth Bale was in beast mode for Tottenham but he was 12th in Ballond'or, only after he went to Real Madrid, his strength got recognized and improved to peak at 6th
In 2013-14, Suarez was in beast mode carrying Liverpool alone, but he was ranked 19th in 2013 Ballon d'Or and was NOT even nominated for 2014 for biting. But after he went to Barcelona, his same-level (or arguably inferior) performance earned him consistent 4th and 5th spots.
Check how undisputedly world class La Liga players and non-Liga players peaked in Ballon d"or rankings:
Salah - 5th
Muller - 6th (2nd best 13th)
Lahm - 6th
van Persie - 7th
De Bruyne - 8th
Terry - 10th
Sweinsteiger - 15th
Vidic - 16th (as a defender winning EPL player of the year)
Thiago Silva - 21st
Scholes - 23th
They are surely not inferior players to the below "La Liga" players who peaked higher:
Cannavaro -1st (with due respect, he had a great 2006 World Cup, but the fact that he played for Real Madrid when the election occurred mattered)
Deco - 2nd
Carlos - 2nd
Neymar - 3rd
Grizemann - 3rd
Falcao - 5th (again with due respect, he had a great 2012 but he was a pure goal scorer who was outscored by van Persie who was a more complete player but ranked 9th)