Do you accept everything that the Catholic Church teaches about faith and morals? If not, then you are “protesting” against some of her teachings, and you need to work through your objections to Catholic doctrine.
It seem to me though, that many of the issues that Protestant converts have to work through is mostly a matter of realizing that what they thought the Catholic Church teaches isn’t what she really teaches. Protestants are raised with a lot of misconceptions about what the Catholic Church actually teaches.
Heck, a lot of Catholics don’t understand what the Catholic Church teaches either. When a misinformed Catholic is a catechist for RCIA, the convert really has a problem coming to know what the Catholic Church actually teaches. If you are having a problem with what a catechist is telling you, ask the catechist to direct you to the section of the Catechism of the Catholic Church that deals with the issue at hand. If the catechist cannot reconcile his teaching with what is in the catechism, then beware of what the catechist is saying.