What do you mean by the long term trend? Since 1959, a collateralized commodity index would have outperformed ALL asset classes, including the S&P500, with less risk.
http://papers.nber.org/papers/w10595
Regardless, Rogers does not advocate commodities as an inherently superior investment, just that they are presently undervalued relative to stocks and bonds. He invests in cyclical macro trends, not long term buy and hold. Since he started the RICI in 1998, the index has outperformed all mutual funds regardless of industry.