Lacking testimony from the Native Americans involved, it is very hard to know the answer to this question. It is hard to know why, for instance, a measles epidemic in what is now Washington led to the deaths of the Whitmans while similar epidemics did not led to the killing of Spanish missionaries. There are, however, at least three factors that might help to explain the different levels of success.
First, the Spanish missionaries were backed by the full weight of the Spanish government. They were not (as the missionaries in Oregon were) mere individuals off to try to save souls. This may have made them seem more important in the eyes of the Native Americans. It might have made the Indians more likely to want to convert to gain access to the wealth and power of the Spaniards.
Second, the Catholics had a monopoly on California. Therefore, they were able to present a single message. The Oregon missionaries were both Catholic and Protestant. The competition between the two might have lowered Native American respect for both.
Finally, the Spanish did not come along with huge numbers of European settlers. It may be that they did not seem like as much of a threat as the Oregon missionaries did. The Oregon missionaries came along with many settlers and might have been seen more as a threat.