Welcome to the Simplefit.org community!
First and foremost, if you've had that knee pain for a while now, pospone no further a visit to your Dr.; even if you think Simplefit won't do any impact on the pain (with it being a "lite" exercise routine) I, personally, wouldn't recommend a gamble on that pain getting any better on it's own.
About the push ups, it takes time, especially if you never got to do them on regular basis; the most important thing is persistence (after seeing the Doc, of course), because, believe me, in no time you're going to be feeling more comfortable doing your routine.
I still can't do a proper pull up to save my life, but I've seen progress on achieving that goal; now, I'm more proficient with push ups than I ever was. Sit ups were never a problem to me, but I've perfected my technic while doing this program.
Once again welcome, and we hope that you keep going with the program for as long as you can. :)