Generally not.
Most cases charge the pen and iPad in direct contact, because for wireless charging to work, the two must be close enough together. Measured about six pages of paper thickness, it can not be charged.
So it is recommended that when you buy a protective case, buy a protective case with a pen slot, which will be slightly wider, but it is not easy to lose the pen. The protective case without a pen slot is good-looking, but it relies on the magnetic pen, which is easy to shake and even lose the pen when actually used.