Is atheism a scientific perspective?

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You're right, the appearance of design might be an illusion, but I have not seen a compelling reason to think it to be so. In fact, the more I learn the more I think it may be genuine. We have those historical examples of times when things were not as they seemed to be, and that should keep us cautious and fair minded when evaluating the appearance of design. However, just because things aren't always as they appear does not mean that they are never as they appear.

I think it depends on how we approach it and what we think we're looking for.  If it's just highly-advanced beings who are not particularly compassionate then the design of things like harmful bacteria or viruses is not surprising (though it might be very disconcerting).  If it's a highly-advanced being who is the very hallmark of compassion, such things should trouble us because it's difficult to see where they fit in.

I understand that for a great many people, the idea that there must be a god is very compelling and makes intuitive sense.  But where we go from there must take into account everything we see in that design, including the stuff that might make us worry about the type of intellect behind it.  I'm cautious about accepting the notion of a highly-advanced --and unbelievably powerful-- being creating everything around us, because some of that stuff is very scary.

Again, I think that some of these scary features of our world that you are referring to can be considered mechanisms to ensure that the genetic integrity is maintained. For example, we have mechanisms to avoid bacterial infections. When we have a poor diet/ lifestyle, we are more susceptible to being overcome by these infections. They may be a mechanism to weed out those who are not living healthy lives.

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It's not an assertion that intelligence is the only known cause, that is true. Nobody knows of an adequate alternative, and intelligence is repeatedly observed to be adequate.

Personally I think that the cause of life is a non-sentient process, and that there's nothing particularly special about what we happen to be -- humans are one possible result of a chain of countless processes, but not necessarily the best result or even an important one.

If you do assume an intelligent agent you just create the same problem at an earlier stage.  Who {or more likely, what} created the creator?

I know that it often follows from the atheist perspective that humans are not important, but the reality is that we are a very important species. We are the only species capable of impacting the world in such a dramatic way. We are changing conditions for all other species and hampering their ability to thrive. The minute we consider ourselves to be just another species is the minute that we will damage the world beyond repair.