The only reason he was taking home the biggest paycheck was that he was now a bankable actor thanks to the Xmen movies. Everyone thought that Patrick Stewart alone would be enough to rake in the money needed to make Star Trek Nemesis a success.
The TNG movies always focussed on Picard and Data, since 1994's Generations. This continued even more so in 1996's First Contact and 1999's Insurrection.
Presumably this had nothing to do with the release of X-Men in 2000, unless the producers of the Star Trek movies could anticipate the fairly modest financial success of the first X-Men movie. The X-Men series only became big hits with the release of X2 (2003), which came, guess what, over 6 months after the release of Nemesis (2002).