When in disgrace with fortune and men's eyes, (1)
As usual, there are a few different ways to interpret Shakespeare's use of the term "fortune." A lot of readers scan this line and just assume the speaker is just down on his luck in general (out of favor with the goddess Fortune, a.k.a. fate). In other words, nothing's going this guy's way. That seems true enough, but we think the line holds another meaning as well. The word "fortune" can also mean "wealth" or "riches," so the speaker might also be hinting that he's down on his financial luck.
And trouble deaf heav'n with my bootless cries, (3)
Okay. "Bootless" literally means useless, so, on the one hand, the speaker is saying that his prayers feel like a waste of time because God doesn't answer them. But, at the same time, the use of the word "bootless" creates an image of poverty—as if the speaker is literally some kind of bootless (shoeless) beggar who is being ignored by God. This reinforces the idea that the speaker is spiritually bankrupt.
Wishing me like to one more rich in hope, (5)
Once again, we have a line that can be read two different ways. On the one hand, the speaker says that he wishes he could be like someone who has a lot more hope (is richer in hope). But, the line can also mean that he wishes he had better prospects (more "hope") of becoming "rich" or wealthy. Shakespeare seems to be asking which kind of wealth is more important, don't you think?