Sure the Charter can be amended, just that it is virtually impossible to do so. And this is not a shortcoming of the Charter, this is its strength.
Human rights, fundamental rights are an integral part of the constitution and must not be subject to the whims of the majority. If the Charter could be amended by say a 50%+1 referendum, then it won’t be democracy any more, it will be the tyranny of the majority. I personally wouldn’t want to live in a country where fundamental rights such as right to free speech, right to vote, right to life, right to freedom of worship etc. can be restricted or taken away completely by a 50%+1 Majority in a referendum.
The Charter, the constitution must be very difficult to amend, as it is in USA and in Canada. That is the strength of the constitution, that it gives a framework of human rights, against which any law is judged, it gives the unvarying, consistent framework from generation to generation.