I can think of two reasons:
1) True cost of transaction. Assuming you are using a foreign credit card, you will get hit with a % surcharge, plus DCC (dynamic currency conversion). This can raise the actual cost, once the transaction is processed, of an additional 5-10%.
2) Recourse in case something goes really awry. You'll be under the laws of the PRC, which aren't particularly customer-favorable. This is even more important now that ctrip has changed its business to an open platform from which hundreds (thousands?) of agencies can use to attract clients. While one can chargeback against foreign credit cards issued under the laws of many developed countries, there is still a cost for disruption of your plans, especially when it happens in real time.

As for the example given by @moondog above, I flatly find it hard to believe that ctrip has that big a differential in ticket price, without something being very very amiss. There's got to be a catch somewhere. If it's too good to be true, it probably isn't. A cautionary tale being the ctrip ticketing scam earlier this year, which I think we referenced on another thread here. If what ctrip is offering is a completely legitimate deal, then you can bet that other OTA's will have the same deal, even if the airlines themselves don't. And seriously, a fairer comparison by moondog would have compared ctrip's price to other OTA prices for the exact same ticket, same dates. The airline.com sites are generally always going to show higher for premium fares so limited the ctrip comparison to those is hardly an accurate apples to apples comparison.