It seems that most Protestant churches are fairly silent on their reasoning; it's something that people don't really think about because it is so ingrained into their worship. However, the Orthodox Presbyterian Church (one of the many, many Protestant denominations) had a Q&A where they discussed crosses in churches. Several key points:
- Their guidelines for worship, the Westminster Standards (Confession of Faith and Catechisms) and the OPC Book of Church Order (BCO), do not have any mention about crosses in church, thus there are no formal guidelines
- Local churches are free to include them or not include them as they see fit
- Given that early churches did not have dedicated meeting places, they did not have crosses as permanent fixtures and yet were still able to worship
To answer your specific questions:
What is the benefit of putting a cross symbol inside the church?
The benefit is whatever the local churches ascribe to it when they ask for it to be installed. The question asker gives a fairly common perspective:
Some say that the cross like the [national] flag, is only symbolic. While the flag is not in the Bible, the cross is. Albeit a method of traditional Roman execution at the time of Christ on earth, without the cross there is no Calvary, no crucifiction and therefore no Christ, who died and shed his blood for us on the cross.
In other words, for some people the cross is a symbol that is representative of something greater. Much like people treat a flag with respect because it represents a nation, the cross is treated with respect and importance because it represents Christ's sacrifice (or Christ himself) and the basis it has on Christian faith.
How did putting a cross inside a church begin and who ordered it?
[W]hen did churches begin to include crosses in their architecture? Now I grant that the question is virtually un-answerable. But it makes a valid point. It was without question a long time before the New Testament churches had their own buildings, and arguably a longer time before they began to fix crosses on the walls.
While I suspect that historians could probably more reliably pinpoint the time that crosses became commonplace, I think the point is that because the early church was persecuted, they wouldn't have been able to hang crosses up. It was pretty commonplace by the time of the Protestant Reformation, and since your question is about Protestantism, I think it's fair to say that nobody "ordered it", instead people just thought it was a natural thing to do.