who did you go with.what are those trays made of.为什么一个用do提问一个用are呢?

因为 Who did you go with? 里面的 go 是主动语态,一般过去时.
用完整的句子回答,是：
I went with Xiao Ming.
此类陈述句改成疑问句,要加 do 的适当形式.
而 what are those trays made of? 里面的be made of,是被动语态,一般现在时.
用完整的句子回答,是：Those trays are made of plastic.
此类陈述句改成疑问句,要把 be 动词提前.