Yes, as with anything - the more you do it the easier it should get. How is it difficult at the moment - making your muscles ache or just tiring, do you mean? Keep at it and it will get easier and hopefully more fun!
The saddle sore should go away through time - it might get tired as you up the distance/time of a run but again you will adapt through time.
The same will probably happen for your knees as your body gets used to the extra work.
As for getting easier it depends on how hard you push yourself - you will likely be able to go faster and for longer but if you put enough effort in it will still feel like a hard workout Tis all good though
If you knee's hurt it may mean you saddle height might need adjusting, when your pedal stroke is at the longest your knee should be slightly bent,which usually means when sat in saddle just your tip toes will touch the ground, oh and padded shorts help a bit too. Also make sure the bike is in good condition as if wheels are off true they will bind on brakes etc. and make get plenty of air in your tyres, which you would probably be as well buying a track pump especially if its a road bike. Tyre pressures might not make it feel easier but you should find you will be quicker.
No As Neilster said, theres a saying on the cyclechat forums - It doesnt get easier, you only get faster!
Again, as IanM has stated, make sure your seat is at the right height and everything is moving freely. Padded shorts/seats I feel actually made my ass ache more, but I started out on a leather seated single speed and now have buns of steel!
I'm 5' 2" and have a mtb and road bike, both women specific and bought to fit, you shouldn't have a problem at that height and a good bike shop will be able to advise on the right bike, seat height etc for you
I bike to work every day and back home my bike is second nature to me it does get easy if your seat is making you sore maybe get another one takes abit of getting used to sitting on a bike seat so best to get one you like sitting on plus do get you bike set up right for your hight as with anyone no matter how big you are it can cause you back problems if its not right biking shouldn't be hard work same as running yoyu have to get used to it using different muscles good luck
I think your first reply from Pamss says it all...
Coming from a cycling background, I'd have to agree that it doesn't get easier, you just get faster...but there is a caveat to that statement which relates to what exactly it is that is/isn't getting any easier? As with running - of which I am an absolute newcomer - you will have objectives and goals which are individually constructed by yourself! So, of course at the same speed for the same distance, it gets easier.
If, on the other hand, you choose to work toward completing a sportive (much like you would a marathon or half-marathon) you will want to up your distance which may mean compromising your speed in order to conserve energy for a longer ride than you've done before. If you want to get involved in road/circuit racing on the other hand, then distance is less of a problem but speed is very much of the essence...so already you switch from objective to objective and your training needs to reflect this.
As for saddle sore and your knees, this could be down - as others have suggested - to geometry issues with frame size and a proper fit. There are a great many dimensions to consider even if you have the correct frame size - your saddle height, how far forward/aft your saddle is along the rails, your reach to the handlebars (look up Ape Index) which is as important as the seat-tube dimension (if not more) and how to correct these things which as well as altering the fore/aft and height of the saddle can also be determined by the length of the stem at the handlebar end.
In addition, how much do your knees bend in your current position? There should be a small allowance for bend in the knee to allow for shock absorption (I'm talking road buzz, not off-road by the way) by perhaps less than 10 degrees (approx). If there is no bend in your knee and it is fully locked out then your behind will wobble interminably from one side of the saddle to the other to compensate for the lack of length you've given yourself which will cause discomfort. At the other extreme you risk damaging your knee from it not being elongated enough! In this sense, saddle height is imperative and can be right or wrong within the range of millimetres, not centimetres!
From a personal perspective (and this may help you potentially), I have probably less than a 10 degree bend at full stretch - foot on pedal in lowest position the crank will afford. This is in part because I've had issues with VMO imbalance and maltracking of the knee cap as a result. The VMO - my inside quad was essentially weaker than the outside quad, caused in part through the fact that the VMO only contracts properly in the last 10-15 degrees of movement and I spent too many years climbing hills sat in the saddle not properly engaging that VMO muscle, whereas what I should have been doing was stretching that leg out as far as I could, out of the saddle!
This is probably too techy but if you can, describe your knee pain specifically to a physio/the forum/your bike fitter.