"Beyond me" means "beyond my comprehension" -- ie, I cannot understand it at all. "It" refers to "the fact that you and Tom can be roommates." If you'd like, you can reverse the order of the clauses so as to eliminate "it:" How you and Tom can be roommates is beyond me. You could also replace "how" with "the fact that -- the meaning would be quite similar:" The fact that you and Tom can be roommates is beyond me.

You can also write as: I wonder how you and Tom can be roommates.

"It is beyond me HOW you and tom can be roomates" & "it is beond me THAT you and tom can be roomates". These two sentences would basically mean the same in most situation. "How" is more of a question and "That" is more of a statement. The tone of the voice slightly changes when saying it in question form or statement form. Hope this helps.

be beyond sb (infml 口) be impossible for sb to imagine, understand or calculate 对於某人来说, 难以想像﹑ 理解或估计: It's beyond me why she wants to marry Geoff. 我不能理解她为什麽要和杰弗结婚. 我很难想象你和Tom怎么成为室友的。 that 可以有可以省略 a roommates 不对 要用复数。