I would imagine it'd be because, if they granted Tibet its independence, foreign powers could seed the new government with operatives that the PRC might not want. Tibet's natural terrain means that rooting out 'terrorist' (And I use the term in the sense of 'Those who attack the Chinese government', these could even be operatives of a foreign government, rather than radical militant cells) organizations would be naturally difficult. And if Tibet were to ally with the enemies of China in any possible war, that'd give China's enemies a strategic point (In which to base airbases and supply depots) that would give them access to the majority of mainland China (with current advances in aeroplane technology). Invading to retake Tibet in the former circumstance (with terrorists attacking mainland China with virtual impunity) would be an act of, in the international community's eyes, 'baseless aggression', and in the latter circumstance, would be made much more difficult by the naturally-defensible terrain and the lack of major routes into Tibet.
In other words, the country would, when independent, be a boon to China's opponents, and a bane to China, itself.