I think you're misunderstanding "Wonderland". It's not simply a place that isn't real - it's a place that's more fantastical than reality, a place where rules don't apply and reality as you know it breaks down. In this film series the robot-infested, scorched-skies, plugging-into-computers, I-know-kung-fu real world is more unbelievable than the dull, rule-based Matrix.
Morpheus is making a parallel between Neo and Alice.
Neo begins his journey to Wonderland by paralleling the book - he follows a White Rabbit and goes on to meet a cast of characters who defy the rules of reality as he knows it. With this context in mind Morpheus's statement is much clearer.
The blue pill
- The story ends: No more Wonderland - just like the end of the book, you'll be back in your old, predictable reality.
- You wake up in your bed: the blue pill is implied to be a sedative. Neo, just like Alice, will wake up back in his normal "reality".
- Believe whatever you want to believe: Neo will be free to make up whatever he wants to explain Morpheus and the events he has seen. Again, this parallels the book - perhaps it was all just a dream.
The red pill
You missed an important part of the quote here - the second part. For context, the first Chapter of Alice in Wonderland (in which she follows the rabbit and begins her journey to Wonderland) is called "Down the Rabbit Hole".
- You stay in Wonderland: You stay in the world I am showing you, where things make no sense.
- I show you how deep the rabbit hole goes: Neo continues in his journey, and Morpheus shows him just how crazy the real world really is.
Hopefully that makes things clearer?